Starting phenix.real_space_refine
on Wed Sep 17 04:46:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqp_45818/09_2025/9cqp_45818.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqp_45818/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqp_45818/09_2025/9cqp_45818.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqp_45818/09_2025/9cqp_45818.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqp_45818/09_2025/9cqp_45818.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqp_45818/09_2025/9cqp_45818.map"
  }
  resolution = 2.78
  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=   0.023
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): 0.01s

  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: 1.48, per 1000 atoms: 0.33
  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: 0.36
  Conformation dependent library (CDL) restraints added in 199.3 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
      88.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  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: 0.70

  Time building geometry restraints manager: 0.50 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: 0.00
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:             3.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.750
  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:7.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.050
-------------------------------------------------------------------------------
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 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:  2.24 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.40 (0.62), residues: 124

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 4610)
  covalent geometry    : angle       0.86826 ( 6330)
  hydrogen bonds       : bond        0.11420 (  343)
  hydrogen bonds       : angle       5.02983 (  978)
  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  : 0.172 
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: 0.7839
  time to fit residues: 52.4237
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  : 0.174 
-------------------------------------------------------------------------------
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 54 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3873 r_free = 0.3873 target = 0.175523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.150408 restraints weight = 3917.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 1.12
r_work: 0.3445 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
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      :  0.005   0.099   4614  Z= 0.145
  Angle     :  0.597   6.841   6330  Z= 0.282
  Chirality :  0.040   0.133    692
  Planarity :  0.006   0.045    790
  Dihedral  : 10.818  80.792    633
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 11.67 %
    Favored  : 85.90 %
  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:  2.68 (0.36), residues: 558
  helix:  2.18 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.40 (0.60), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 104 
 TYR   0.006   0.001   TYR B 130 
 PHE   0.009   0.001   PHE B  85 
 TRP   0.010   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 4610)
  covalent geometry    : angle       0.59691 ( 6330)
  hydrogen bonds       : bond        0.03982 (  343)
  hydrogen bonds       : angle       4.25716 (  978)
  Misc. bond           : bond        0.08901 (    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
  60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6390 (mtt)
REVERT: A   99 LYS cc_start: 0.8133 (mttm) cc_final: 0.7826 (mtmt)
REVERT: B   22 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6283 (tp30)
REVERT: B   66 LYS cc_start: 0.7687 (mmmm) cc_final: 0.7198 (mttt)
REVERT: B   95 LYS cc_start: 0.7861 (tmtt) cc_final: 0.7113 (mptt)
REVERT: B  104 ARG cc_start: 0.7428 (ttp80) cc_final: 0.6241 (mpt180)
REVERT: C   61 LYS cc_start: 0.8183 (mttt) cc_final: 0.7663 (mtpt)
REVERT: C   76 MET cc_start: 0.6926 (mtt) cc_final: 0.6392 (mtt)
REVERT: C   99 LYS cc_start: 0.8175 (mttp) cc_final: 0.7873 (mtmt)
REVERT: D   66 LYS cc_start: 0.7724 (mmmm) cc_final: 0.7262 (mttt)
REVERT: D   95 LYS cc_start: 0.7990 (tttt) cc_final: 0.7207 (mptt)
REVERT: D  104 ARG cc_start: 0.7408 (ttp80) cc_final: 0.6204 (mpt180)
REVERT: D  120 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6959 (tttm)
  outliers start: 11
  outliers final: 2
  residues processed: 58
  average time/residue: 0.8448
  time to fit residues: 50.3669
Evaluate side-chains
  49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
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 43 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0070
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.174179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.149354 restraints weight = 3912.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.11
r_work: 0.3427 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.097   4614  Z= 0.145
  Angle     :  0.586   6.553   6330  Z= 0.275
  Chirality :  0.040   0.127    692
  Planarity :  0.006   0.047    790
  Dihedral  :  9.568  78.171    622
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.11 %
    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 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:  2.59 (0.36), residues: 558
  helix:  2.12 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.35 (0.58), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D  40 
 TYR   0.006   0.001   TYR D  35 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.011   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 4610)
  covalent geometry    : angle       0.58593 ( 6330)
  hydrogen bonds       : bond        0.03883 (  343)
  hydrogen bonds       : angle       4.14012 (  978)
  Misc. bond           : bond        0.09191 (    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
  62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6546 (mtt)
REVERT: A   99 LYS cc_start: 0.8165 (mttm) cc_final: 0.7860 (mtmt)
REVERT: B   66 LYS cc_start: 0.7701 (mmmm) cc_final: 0.7211 (mttt)
REVERT: B   95 LYS cc_start: 0.7927 (tmtt) cc_final: 0.7269 (mptt)
REVERT: B  104 ARG cc_start: 0.7501 (ttp80) cc_final: 0.6309 (mpt180)
REVERT: B  121 GLU cc_start: 0.7617 (pm20) cc_final: 0.7349 (pm20)
REVERT: B  132 LYS cc_start: 0.8145 (ptmt) cc_final: 0.7679 (ptpt)
REVERT: C   61 LYS cc_start: 0.8167 (mttt) cc_final: 0.7684 (mtpt)
REVERT: C   76 MET cc_start: 0.7052 (mtt) cc_final: 0.6645 (mtt)
REVERT: C   99 LYS cc_start: 0.8176 (mttp) cc_final: 0.7898 (mtmt)
REVERT: C  127 LYS cc_start: 0.7406 (mtmt) cc_final: 0.7031 (mttt)
REVERT: D   66 LYS cc_start: 0.7757 (mmmm) cc_final: 0.7086 (mttt)
REVERT: D   95 LYS cc_start: 0.7969 (tttt) cc_final: 0.7260 (mptt)
REVERT: D  104 ARG cc_start: 0.7489 (ttp80) cc_final: 0.6260 (mpt180)
REVERT: D  120 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6946 (tttp)
  outliers start: 8
  outliers final: 3
  residues processed: 59
  average time/residue: 0.8984
  time to fit residues: 54.3816
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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 53 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 21 optimal weight:    0.3980
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 24 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3847 r_free = 0.3847 target = 0.173066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.147763 restraints weight = 3915.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.13
r_work: 0.3428 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.098   4614  Z= 0.143
  Angle     :  0.585   6.593   6330  Z= 0.274
  Chirality :  0.040   0.137    692
  Planarity :  0.005   0.048    790
  Dihedral  :  9.356  76.283    622
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.11 %
    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 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:  2.52 (0.36), residues: 558
  helix:  2.10 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.21 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 104 
 TYR   0.005   0.001   TYR D  35 
 PHE   0.012   0.001   PHE D 118 
 TRP   0.011   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 4610)
  covalent geometry    : angle       0.58543 ( 6330)
  hydrogen bonds       : bond        0.03804 (  343)
  hydrogen bonds       : angle       4.10702 (  978)
  Misc. bond           : bond        0.09295 (    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
  63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6516 (mtt)
REVERT: A   99 LYS cc_start: 0.8142 (mttm) cc_final: 0.7803 (mtmt)
REVERT: B   66 LYS cc_start: 0.7652 (mmmm) cc_final: 0.7124 (mttt)
REVERT: B   95 LYS cc_start: 0.7905 (tmtt) cc_final: 0.7233 (mptt)
REVERT: B  104 ARG cc_start: 0.7458 (ttp80) cc_final: 0.6199 (mpt180)
REVERT: C   61 LYS cc_start: 0.8081 (mttt) cc_final: 0.7593 (mtpt)
REVERT: C   76 MET cc_start: 0.7093 (mtt) cc_final: 0.6752 (mtt)
REVERT: C   99 LYS cc_start: 0.8126 (mttp) cc_final: 0.7829 (mtmt)
REVERT: D   66 LYS cc_start: 0.7705 (mmmm) cc_final: 0.7182 (mttt)
REVERT: D   95 LYS cc_start: 0.7962 (tttt) cc_final: 0.7273 (mptt)
REVERT: D  104 ARG cc_start: 0.7427 (ttp80) cc_final: 0.6136 (mpt180)
REVERT: D  120 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6852 (tttp)
  outliers start: 10
  outliers final: 2
  residues processed: 59
  average time/residue: 0.8352
  time to fit residues: 50.7003
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  : 0.213 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    0.1980
   chunk 28 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0570
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.175848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.151160 restraints weight = 3905.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 1.10
r_work: 0.3456 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   4614  Z= 0.120
  Angle     :  0.562   6.665   6330  Z= 0.261
  Chirality :  0.038   0.120    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.170  76.432    622
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.44 %
    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 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:  2.27 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.12 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.005   0.001   TYR D  35 
 PHE   0.013   0.001   PHE D 118 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 4610)
  covalent geometry    : angle       0.56161 ( 6330)
  hydrogen bonds       : bond        0.03387 (  343)
  hydrogen bonds       : angle       3.97523 (  978)
  Misc. bond           : bond        0.07041 (    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
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6561 (mtt)
REVERT: A   99 LYS cc_start: 0.8137 (mttm) cc_final: 0.7824 (mtmt)
REVERT: B   66 LYS cc_start: 0.7699 (mmmm) cc_final: 0.7222 (mttt)
REVERT: B   95 LYS cc_start: 0.7918 (tmtt) cc_final: 0.7333 (mptt)
REVERT: B  104 ARG cc_start: 0.7442 (ttp80) cc_final: 0.6291 (mpt180)
REVERT: C   61 LYS cc_start: 0.8104 (mttt) cc_final: 0.7642 (mtpt)
REVERT: C   76 MET cc_start: 0.7102 (mtt) cc_final: 0.6784 (mtt)
REVERT: C   99 LYS cc_start: 0.8155 (mttp) cc_final: 0.7858 (mtmt)
REVERT: D   66 LYS cc_start: 0.7740 (mmmm) cc_final: 0.7263 (mtmt)
REVERT: D   95 LYS cc_start: 0.7946 (tttt) cc_final: 0.7311 (mptt)
REVERT: D  104 ARG cc_start: 0.7406 (ttp80) cc_final: 0.6210 (mpt180)
REVERT: D  120 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6983 (tttp)
  outliers start: 9
  outliers final: 3
  residues processed: 56
  average time/residue: 0.8167
  time to fit residues: 47.0476
Evaluate side-chains
  51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0870
   chunk 22 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 47 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0970
   overall best weight:    0.3356

-------------------------------------------------------------------------------
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 = 0.3891 r_free = 0.3891 target = 0.177277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.152302 restraints weight = 3943.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.13
r_work: 0.3475 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087   4614  Z= 0.111
  Angle     :  0.547   6.579   6330  Z= 0.252
  Chirality :  0.038   0.127    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.043  77.059    622
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.66 %
    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 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:  2.40 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.10 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  40 
 TYR   0.005   0.001   TYR D 130 
 PHE   0.012   0.001   PHE D 118 
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4610)
  covalent geometry    : angle       0.54712 ( 6330)
  hydrogen bonds       : bond        0.03158 (  343)
  hydrogen bonds       : angle       3.88289 (  978)
  Misc. bond           : bond        0.06242 (    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
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6621 (mtt)
REVERT: A   99 LYS cc_start: 0.8109 (mttm) cc_final: 0.7798 (mtmt)
REVERT: B   66 LYS cc_start: 0.7679 (mmmm) cc_final: 0.7196 (mttt)
REVERT: B   68 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7248 (mp)
REVERT: B   95 LYS cc_start: 0.7890 (tmtt) cc_final: 0.7309 (mptt)
REVERT: B  104 ARG cc_start: 0.7384 (ttp80) cc_final: 0.6235 (mpt180)
REVERT: C   61 LYS cc_start: 0.8074 (mttt) cc_final: 0.7629 (mtpt)
REVERT: C   76 MET cc_start: 0.7134 (mtt) cc_final: 0.6838 (mtt)
REVERT: C   99 LYS cc_start: 0.8122 (mttp) cc_final: 0.7825 (mtmt)
REVERT: D   66 LYS cc_start: 0.7691 (mmmm) cc_final: 0.7194 (mtmt)
REVERT: D   68 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7227 (mp)
REVERT: D   95 LYS cc_start: 0.7920 (tttt) cc_final: 0.7321 (mptt)
REVERT: D  104 ARG cc_start: 0.7355 (ttp80) cc_final: 0.6159 (mpt180)
REVERT: D  120 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6952 (tttp)
  outliers start: 9
  outliers final: 2
  residues processed: 56
  average time/residue: 0.7489
  time to fit residues: 43.2304
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   68 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 23 optimal weight:    0.2980
   chunk 52 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.173674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.147880 restraints weight = 3980.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.16
r_work: 0.3425 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.117   4614  Z= 0.142
  Angle     :  0.581   6.252   6330  Z= 0.271
  Chirality :  0.040   0.124    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.132  74.997    622
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.00 %
    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 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:  2.63 (0.36), residues: 558
  helix:  2.23 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.04 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.005   0.001   TYR D 130 
 PHE   0.012   0.001   PHE D 118 
 TRP   0.010   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4610)
  covalent geometry    : angle       0.58120 ( 6330)
  hydrogen bonds       : bond        0.03794 (  343)
  hydrogen bonds       : angle       4.06246 (  978)
  Misc. bond           : bond        0.10216 (    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
  61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6591 (mtt)
REVERT: A   99 LYS cc_start: 0.8157 (mttm) cc_final: 0.7815 (mtmt)
REVERT: B   66 LYS cc_start: 0.7656 (mmmm) cc_final: 0.6947 (mttt)
REVERT: B   95 LYS cc_start: 0.7957 (tmtt) cc_final: 0.7342 (mptt)
REVERT: B  104 ARG cc_start: 0.7474 (ttp80) cc_final: 0.6224 (mpt180)
REVERT: C   61 LYS cc_start: 0.8069 (mttt) cc_final: 0.7614 (mtpt)
REVERT: C   76 MET cc_start: 0.7156 (mtt) cc_final: 0.6873 (mtt)
REVERT: C   99 LYS cc_start: 0.8131 (mttp) cc_final: 0.7838 (mtmt)
REVERT: D   66 LYS cc_start: 0.7711 (mmmm) cc_final: 0.7019 (mttt)
REVERT: D   68 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7188 (mp)
REVERT: D   95 LYS cc_start: 0.7924 (tttt) cc_final: 0.7302 (mptt)
REVERT: D  104 ARG cc_start: 0.7439 (ttp80) cc_final: 0.6160 (mpt180)
REVERT: D  120 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6918 (tttp)
  outliers start: 9
  outliers final: 4
  residues processed: 59
  average time/residue: 0.7992
  time to fit residues: 48.5321
Evaluate side-chains
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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   68 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 36 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0040
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.4992

-------------------------------------------------------------------------------
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 = 0.3940 r_free = 0.3940 target = 0.179541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.159490 restraints weight = 3931.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 0.92
r_work: 0.3488 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103   4614  Z= 0.125
  Angle     :  0.565   6.373   6330  Z= 0.263
  Chirality :  0.039   0.119    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.074  75.335    622
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.88 %
    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 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:  2.30 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop : -0.01 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.005   0.001   TYR D 130 
 PHE   0.010   0.001   PHE D 118 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4610)
  covalent geometry    : angle       0.56547 ( 6330)
  hydrogen bonds       : bond        0.03481 (  343)
  hydrogen bonds       : angle       4.00485 (  978)
  Misc. bond           : bond        0.08123 (    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
  61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6677 (mtt)
REVERT: A   99 LYS cc_start: 0.8140 (mttm) cc_final: 0.7862 (mtmt)
REVERT: B   66 LYS cc_start: 0.7736 (mmmm) cc_final: 0.7282 (mtmt)
REVERT: B   95 LYS cc_start: 0.7932 (tmtt) cc_final: 0.7419 (mptt)
REVERT: B  104 ARG cc_start: 0.7482 (ttp80) cc_final: 0.6370 (mpt180)
REVERT: C   61 LYS cc_start: 0.8094 (mttt) cc_final: 0.7685 (mtpt)
REVERT: C   76 MET cc_start: 0.7202 (mtt) cc_final: 0.6929 (mtt)
REVERT: C   99 LYS cc_start: 0.8165 (mttp) cc_final: 0.7901 (mtmt)
REVERT: D   66 LYS cc_start: 0.7772 (mmmm) cc_final: 0.7338 (mtmt)
REVERT: D   68 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7282 (mp)
REVERT: D   95 LYS cc_start: 0.7952 (tttt) cc_final: 0.7415 (mptt)
REVERT: D  104 ARG cc_start: 0.7455 (ttp80) cc_final: 0.6314 (mpt180)
REVERT: D  120 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.7033 (tttp)
  outliers start: 9
  outliers final: 2
  residues processed: 58
  average time/residue: 0.7829
  time to fit residues: 46.7286
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  : 0.218 
-------------------------------------------------------------------------------
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   68 LEU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0020
   chunk 32 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5788

-------------------------------------------------------------------------------
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 = 0.3848 r_free = 0.3848 target = 0.173556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.148462 restraints weight = 3925.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.12
r_work: 0.3440 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.113   4614  Z= 0.135
  Angle     :  0.576   6.083   6330  Z= 0.268
  Chirality :  0.039   0.121    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.077  74.513    622
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.54 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.62 (0.36), residues: 558
  helix:  2.24 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop : -0.05 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  92 
 TYR   0.005   0.001   TYR D 130 
 PHE   0.011   0.001   PHE D 118 
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4610)
  covalent geometry    : angle       0.57573 ( 6330)
  hydrogen bonds       : bond        0.03650 (  343)
  hydrogen bonds       : angle       4.05017 (  978)
  Misc. bond           : bond        0.09355 (    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
  58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6703 (mtt)
REVERT: A   99 LYS cc_start: 0.8157 (mttm) cc_final: 0.7825 (mtmt)
REVERT: B   66 LYS cc_start: 0.7677 (mmmm) cc_final: 0.7165 (mtmt)
REVERT: B   95 LYS cc_start: 0.7915 (tmtt) cc_final: 0.7360 (mptt)
REVERT: B  104 ARG cc_start: 0.7466 (ttp80) cc_final: 0.6244 (mpt180)
REVERT: C   61 LYS cc_start: 0.8073 (mttt) cc_final: 0.7632 (mtpt)
REVERT: C   76 MET cc_start: 0.7230 (mtt) cc_final: 0.6978 (mtt)
REVERT: C   99 LYS cc_start: 0.8140 (mttp) cc_final: 0.7846 (mtmt)
REVERT: D   66 LYS cc_start: 0.7730 (mmmm) cc_final: 0.7233 (mtmt)
REVERT: D   68 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7199 (mp)
REVERT: D   95 LYS cc_start: 0.7935 (tttt) cc_final: 0.7335 (mptt)
REVERT: D  104 ARG cc_start: 0.7437 (ttp80) cc_final: 0.6184 (mpt180)
REVERT: D  120 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6936 (tptp)
  outliers start: 9
  outliers final: 3
  residues processed: 55
  average time/residue: 0.8105
  time to fit residues: 45.8715
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  : 0.174 
-------------------------------------------------------------------------------
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   68 LEU
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 43 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 55 optimal weight:    0.4980
   chunk 1 optimal weight:    0.0370
   chunk 48 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 44 optimal weight:    0.2980
   chunk 34 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.4458

-------------------------------------------------------------------------------
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 = 0.4121 r_free = 0.4121 target = 0.193100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.170333 restraints weight = 3523.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 1.06
r_work: 0.3637 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.101   4614  Z= 0.122
  Angle     :  0.566   6.166   6330  Z= 0.262
  Chirality :  0.038   0.117    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.013  75.262    622
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.98 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.72 (0.36), residues: 558
  helix:  2.33 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop : -0.07 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 104 
 TYR   0.005   0.001   TYR D 130 
 PHE   0.011   0.001   PHE D 118 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.004   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4610)
  covalent geometry    : angle       0.56556 ( 6330)
  hydrogen bonds       : bond        0.03376 (  343)
  hydrogen bonds       : angle       3.97988 (  978)
  Misc. bond           : bond        0.07940 (    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
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A   99 LYS cc_start: 0.8082 (mttm) cc_final: 0.7767 (mtmt)
REVERT: B   66 LYS cc_start: 0.7687 (mmmm) cc_final: 0.7178 (mtmt)
REVERT: B   95 LYS cc_start: 0.7920 (tmtt) cc_final: 0.7401 (mptt)
REVERT: B  104 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6295 (mpt180)
REVERT: C   61 LYS cc_start: 0.8057 (mttt) cc_final: 0.7604 (mtpt)
REVERT: C   76 MET cc_start: 0.7215 (mtt) cc_final: 0.6993 (mtt)
REVERT: C   99 LYS cc_start: 0.8107 (mttp) cc_final: 0.7815 (mtmt)
REVERT: D   66 LYS cc_start: 0.7712 (mmmm) cc_final: 0.7236 (mtmt)
REVERT: D   68 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7172 (mp)
REVERT: D   95 LYS cc_start: 0.7942 (tttt) cc_final: 0.7394 (mptt)
REVERT: D  104 ARG cc_start: 0.7424 (ttp80) cc_final: 0.6234 (mpt180)
REVERT: D  120 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6934 (tttp)
  outliers start: 7
  outliers final: 3
  residues processed: 55
  average time/residue: 0.8218
  time to fit residues: 46.5254
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  : 0.209 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.4980
   chunk 31 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0060
   chunk 46 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4396

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.194030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.173607 restraints weight = 3499.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 0.94
r_work: 0.3660 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2071

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= 0.122
  Angle     :  0.568   6.086   6330  Z= 0.264
  Chirality :  0.038   0.122    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.021  75.432    622
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.54 %
    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 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:  2.33 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop : -0.03 (0.56), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 104 
 TYR   0.005   0.001   TYR D 130 
 PHE   0.011   0.001   PHE D 118 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4610)
  covalent geometry    : angle       0.56780 ( 6330)
  hydrogen bonds       : bond        0.03400 (  343)
  hydrogen bonds       : angle       3.98085 (  978)
  Misc. bond           : bond        0.08279 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1887.58 seconds
wall clock time: 33 minutes 3.87 seconds (1983.87 seconds total)