Starting phenix.real_space_refine
on Sat May 10 00:58:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqp_45818/05_2025/9cqp_45818.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqp_45818/05_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_45818/05_2025/9cqp_45818.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqp_45818/05_2025/9cqp_45818.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqp_45818/05_2025/9cqp_45818.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqp_45818/05_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-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4470
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "C"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.03, per 1000 atoms: 0.90
  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: 1.32
  Conformation dependent library (CDL) restraints added in 585.1 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: 0.48
  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: 1.23

  Time building geometry restraints manager: 1.52 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:             3.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.140
  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:11.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.550
-------------------------------------------------------------------------------
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  : 0.480 
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: 1.5477
  time to fit residues: 103.7271
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  : 0.577 
-------------------------------------------------------------------------------
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 = 45)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.152367 restraints weight = 3866.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 1.13
r_work: 0.3470 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
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  : 0.464 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6388 (mtt)
REVERT: A   99 LYS cc_start: 0.8086 (mttm) cc_final: 0.7763 (mtmt)
REVERT: B   22 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6290 (tp30)
REVERT: B   66 LYS cc_start: 0.7621 (mmmm) cc_final: 0.7132 (mttt)
REVERT: B   95 LYS cc_start: 0.7885 (tmtt) cc_final: 0.7144 (mptt)
REVERT: B  104 ARG cc_start: 0.7362 (ttp80) cc_final: 0.6189 (mpt180)
REVERT: C   61 LYS cc_start: 0.8131 (mttt) cc_final: 0.7611 (mtpt)
REVERT: C   76 MET cc_start: 0.6837 (mtt) cc_final: 0.6260 (mtt)
REVERT: C   99 LYS cc_start: 0.8143 (mttp) cc_final: 0.7824 (mtmt)
REVERT: D   22 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6703 (mp0)
REVERT: D   66 LYS cc_start: 0.7637 (mmmm) cc_final: 0.7172 (mttt)
REVERT: D   95 LYS cc_start: 0.7976 (tttt) cc_final: 0.7159 (mptt)
REVERT: D  104 ARG cc_start: 0.7345 (ttp80) cc_final: 0.6130 (mpt180)
REVERT: D  120 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6919 (tttm)
  outliers start: 12
  outliers final: 2
  residues processed: 61
  average time/residue: 1.6586
  time to fit residues: 104.2500
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  : 0.487 
-------------------------------------------------------------------------------
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:    0.0020
   chunk 5 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0670
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6130

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.175023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.149518 restraints weight = 3877.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.14
r_work: 0.3438 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092   4614  Z= 0.137
  Angle     :  0.577   6.461   6330  Z= 0.271
  Chirality :  0.039   0.125    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.591  78.774    622
  Min Nonbonded Distance : 2.485

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:  2.71 (0.36), residues: 558
  helix:  2.22 (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   0.004   0.001   HIS C 112 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.006   0.001   TYR D  35 
 ARG   0.004   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  343)
  hydrogen bonds       : angle       4.09366 (  978)
  covalent geometry    : bond        0.00357 ( 4610)
  covalent geometry    : angle       0.57701 ( 6330)
  Misc. bond           : bond        0.08772 (    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
  58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6507 (mtt)
REVERT: A   99 LYS cc_start: 0.8133 (mttm) cc_final: 0.7814 (mtmt)
REVERT: B   66 LYS cc_start: 0.7656 (mmmm) cc_final: 0.7158 (mttt)
REVERT: B   95 LYS cc_start: 0.7912 (tmtt) cc_final: 0.7234 (mptt)
REVERT: B  104 ARG cc_start: 0.7447 (ttp80) cc_final: 0.6247 (mpt180)
REVERT: C   61 LYS cc_start: 0.8120 (mttt) cc_final: 0.7628 (mtpt)
REVERT: C   76 MET cc_start: 0.7019 (mtt) cc_final: 0.6815 (mtt)
REVERT: C   99 LYS cc_start: 0.8146 (mttp) cc_final: 0.7858 (mtmt)
REVERT: C  127 LYS cc_start: 0.7407 (mtmt) cc_final: 0.7022 (mttt)
REVERT: D   66 LYS cc_start: 0.7709 (mmmm) cc_final: 0.7034 (mttt)
REVERT: D   95 LYS cc_start: 0.7972 (tttt) cc_final: 0.7241 (mptt)
REVERT: D  104 ARG cc_start: 0.7428 (ttp80) cc_final: 0.6187 (mpt180)
REVERT: D  120 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6843 (tttp)
  outliers start: 9
  outliers final: 3
  residues processed: 55
  average time/residue: 1.8031
  time to fit residues: 102.2542
Evaluate side-chains
  52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.168174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.142639 restraints weight = 3947.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.14
r_work: 0.3373 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.158   4614  Z= 0.215
  Angle     :  0.671   6.022   6330  Z= 0.319
  Chirality :  0.045   0.135    692
  Planarity :  0.006   0.051    790
  Dihedral  :  9.664  73.848    622
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.78 %
    Favored  : 85.46 %
  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:  1.97 (0.35), residues: 558
  helix:  1.67 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.13 (0.57), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  14 
 HIS   0.005   0.001   HIS C  89 
 PHE   0.018   0.002   PHE B  85 
 TYR   0.005   0.001   TYR D 130 
 ARG   0.002   0.001   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04952 (  343)
  hydrogen bonds       : angle       4.41506 (  978)
  covalent geometry    : bond        0.00560 ( 4610)
  covalent geometry    : angle       0.67126 ( 6330)
  Misc. bond           : bond        0.14364 (    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
  62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A   76 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6566 (mtt)
REVERT: A   99 LYS cc_start: 0.8215 (mttm) cc_final: 0.7872 (mtmt)
REVERT: B   66 LYS cc_start: 0.7757 (mmmm) cc_final: 0.7070 (mttt)
REVERT: B   95 LYS cc_start: 0.7985 (tmtt) cc_final: 0.7314 (mptt)
REVERT: B  104 ARG cc_start: 0.7571 (ttp80) cc_final: 0.6301 (mpt180)
REVERT: B  121 GLU cc_start: 0.7750 (pm20) cc_final: 0.7470 (pm20)
REVERT: B  132 LYS cc_start: 0.8199 (ptmt) cc_final: 0.7708 (ptpt)
REVERT: C   61 LYS cc_start: 0.8144 (mttt) cc_final: 0.7665 (mtpt)
REVERT: C   76 MET cc_start: 0.7158 (mtt) cc_final: 0.6823 (mtt)
REVERT: C   99 LYS cc_start: 0.8217 (mttp) cc_final: 0.7912 (mtmt)
REVERT: D   66 LYS cc_start: 0.7825 (mmmm) cc_final: 0.7102 (mttt)
REVERT: D   95 LYS cc_start: 0.7930 (tttt) cc_final: 0.7240 (mptt)
REVERT: D  104 ARG cc_start: 0.7557 (ttp80) cc_final: 0.6241 (mpt180)
REVERT: D  120 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6918 (tttp)
  outliers start: 8
  outliers final: 3
  residues processed: 59
  average time/residue: 1.6228
  time to fit residues: 98.5627
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  : 0.505 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 11 optimal weight:    0.0970
   chunk 27 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0980
   chunk 1 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0050
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0970
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.1790

-------------------------------------------------------------------------------
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**
A 122 HIS
C  89 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 = 0.3891 r_free = 0.3891 target = 0.178210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.153008 restraints weight = 3943.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 1.15
r_work: 0.3484 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4614  Z= 0.102
  Angle     :  0.543   6.818   6330  Z= 0.248
  Chirality :  0.036   0.111    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.104  76.094    622
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  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:  2.86 (0.36), residues: 558
  helix:  2.37 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.22 (0.57), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 117 
 PHE   0.013   0.001   PHE D 118 
 TYR   0.005   0.001   TYR D 130 
 ARG   0.002   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02907 (  343)
  hydrogen bonds       : angle       3.86632 (  978)
  covalent geometry    : bond        0.00252 ( 4610)
  covalent geometry    : angle       0.54330 ( 6330)
  Misc. bond           : bond        0.02831 (    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
  61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6811 (mmt) cc_final: 0.6585 (mtt)
REVERT: A   99 LYS cc_start: 0.8085 (mttm) cc_final: 0.7757 (mtmt)
REVERT: B   22 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6328 (mm-30)
REVERT: B   66 LYS cc_start: 0.7602 (mmmm) cc_final: 0.7105 (mttt)
REVERT: B   95 LYS cc_start: 0.7912 (tmtt) cc_final: 0.7312 (mptt)
REVERT: C   61 LYS cc_start: 0.8044 (mttt) cc_final: 0.7591 (mtpt)
REVERT: C   76 MET cc_start: 0.7038 (mtt) cc_final: 0.6719 (mtt)
REVERT: C   99 LYS cc_start: 0.8126 (mttp) cc_final: 0.7808 (mtmt)
REVERT: D   22 GLU cc_start: 0.7074 (mm-30) cc_final: 0.5998 (pt0)
REVERT: D   66 LYS cc_start: 0.7666 (mmmm) cc_final: 0.7236 (mtmt)
REVERT: D   95 LYS cc_start: 0.7983 (tttt) cc_final: 0.7342 (mptt)
REVERT: D  120 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6869 (tttp)
  outliers start: 7
  outliers final: 1
  residues processed: 58
  average time/residue: 1.3964
  time to fit residues: 83.8620
Evaluate side-chains
  51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0970
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.173564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.148219 restraints weight = 3903.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 1.13
r_work: 0.3430 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.114   4614  Z= 0.142
  Angle     :  0.582   6.358   6330  Z= 0.273
  Chirality :  0.040   0.128    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.185  75.392    622
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  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 (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:  2.66 (0.36), residues: 558
  helix:  2.24 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.07 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C 112 
 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        0.03797 (  343)
  hydrogen bonds       : angle       4.04158 (  978)
  covalent geometry    : bond        0.00369 ( 4610)
  covalent geometry    : angle       0.58249 ( 6330)
  Misc. bond           : bond        0.09741 (    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
  56 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6569 (mtt)
REVERT: A   99 LYS cc_start: 0.8168 (mttm) cc_final: 0.7840 (mtmt)
REVERT: B   66 LYS cc_start: 0.7664 (mmmm) cc_final: 0.7168 (mtmt)
REVERT: B   95 LYS cc_start: 0.7929 (tmtt) cc_final: 0.7341 (mptt)
REVERT: B  104 ARG cc_start: 0.7488 (ttp80) cc_final: 0.6266 (mpt180)
REVERT: B  121 GLU cc_start: 0.7576 (pm20) cc_final: 0.7280 (pm20)
REVERT: C   61 LYS cc_start: 0.8100 (mttt) cc_final: 0.7627 (mtpt)
REVERT: C   76 MET cc_start: 0.7191 (mtt) cc_final: 0.6867 (mtt)
REVERT: C   99 LYS cc_start: 0.8185 (mttp) cc_final: 0.7883 (mtmt)
REVERT: D   66 LYS cc_start: 0.7715 (mmmm) cc_final: 0.7231 (mtmt)
REVERT: D   68 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7188 (mp)
REVERT: D   95 LYS cc_start: 0.7953 (tttt) cc_final: 0.7324 (mptt)
REVERT: D  104 ARG cc_start: 0.7463 (ttp80) cc_final: 0.6209 (mpt180)
REVERT: D  120 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6930 (tttp)
  outliers start: 9
  outliers final: 2
  residues processed: 54
  average time/residue: 1.5944
  time to fit residues: 88.7687
Evaluate side-chains
  52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  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 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 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0030
   chunk 45 optimal weight:    0.2980
   chunk 25 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.4590

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.175611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.150754 restraints weight = 3926.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 1.11
r_work: 0.3454 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099   4614  Z= 0.122
  Angle     :  0.561   6.589   6330  Z= 0.260
  Chirality :  0.038   0.119    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.087  75.620    622
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.88 %
    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:  2.74 (0.36), residues: 558
  helix:  2.31 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.03 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   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 B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03405 (  343)
  hydrogen bonds       : angle       3.97037 (  978)
  covalent geometry    : bond        0.00318 ( 4610)
  covalent geometry    : angle       0.56094 ( 6330)
  Misc. bond           : bond        0.07759 (    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
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6617 (mtt)
REVERT: A   99 LYS cc_start: 0.8131 (mttm) cc_final: 0.7818 (mtmt)
REVERT: B   66 LYS cc_start: 0.7692 (mmmm) cc_final: 0.7194 (mtmt)
REVERT: B   95 LYS cc_start: 0.7937 (tmtt) cc_final: 0.7348 (mptt)
REVERT: B  104 ARG cc_start: 0.7443 (ttp80) cc_final: 0.6270 (mpt180)
REVERT: B  121 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7330 (pm20)
REVERT: C   61 LYS cc_start: 0.8061 (mttt) cc_final: 0.7625 (mtpt)
REVERT: C   76 MET cc_start: 0.7154 (mtt) cc_final: 0.6863 (mtt)
REVERT: C   99 LYS cc_start: 0.8158 (mttp) cc_final: 0.7854 (mtmt)
REVERT: D   66 LYS cc_start: 0.7725 (mmmm) cc_final: 0.7247 (mtmt)
REVERT: D   68 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7218 (mp)
REVERT: D   95 LYS cc_start: 0.7927 (tttt) cc_final: 0.7323 (mptt)
REVERT: D  104 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6188 (mpt180)
REVERT: D  120 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6963 (tttp)
  outliers start: 8
  outliers final: 2
  residues processed: 55
  average time/residue: 1.6547
  time to fit residues: 93.9714
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  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  121 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3851 r_free = 0.3851 target = 0.172867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.148616 restraints weight = 3898.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.08
r_work: 0.3432 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.123   4614  Z= 0.152
  Angle     :  0.595   6.547   6330  Z= 0.279
  Chirality :  0.041   0.125    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.177  73.450    622
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.54 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.36), residues: 558
  helix:  2.14 (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   0.011   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C 112 
 PHE   0.011   0.001   PHE D 118 
 TYR   0.005   0.001   TYR D  35 
 ARG   0.002   0.001   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03964 (  343)
  hydrogen bonds       : angle       4.12099 (  978)
  covalent geometry    : bond        0.00400 ( 4610)
  covalent geometry    : angle       0.59500 ( 6330)
  Misc. bond           : bond        0.10913 (    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
  60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6608 (mtt)
REVERT: A   99 LYS cc_start: 0.8175 (mttm) cc_final: 0.7863 (mtmt)
REVERT: B   66 LYS cc_start: 0.7756 (mmmm) cc_final: 0.7047 (mttt)
REVERT: B   95 LYS cc_start: 0.7958 (tmtt) cc_final: 0.7353 (mptt)
REVERT: B  104 ARG cc_start: 0.7528 (ttp80) cc_final: 0.6309 (mpt180)
REVERT: C   61 LYS cc_start: 0.8091 (mttt) cc_final: 0.7664 (mtpt)
REVERT: C   76 MET cc_start: 0.7204 (mtt) cc_final: 0.6927 (mtt)
REVERT: C   99 LYS cc_start: 0.8196 (mttp) cc_final: 0.7917 (mtmt)
REVERT: D   66 LYS cc_start: 0.7780 (mmmm) cc_final: 0.7102 (mttt)
REVERT: D   68 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7212 (mp)
REVERT: D   95 LYS cc_start: 0.7978 (tttt) cc_final: 0.7374 (mptt)
REVERT: D  104 ARG cc_start: 0.7483 (ttp80) cc_final: 0.6244 (mpt180)
REVERT: D  120 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6973 (tttp)
  outliers start: 10
  outliers final: 4
  residues processed: 56
  average time/residue: 1.6383
  time to fit residues: 94.5025
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  : 0.431 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0970
   chunk 1 optimal weight:    0.4980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3861 r_free = 0.3861 target = 0.174238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.149636 restraints weight = 3951.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 1.09
r_work: 0.3447 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   4614  Z= 0.131
  Angle     :  0.575   6.782   6330  Z= 0.268
  Chirality :  0.039   0.119    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.104  74.335    622
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.20 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.36), residues: 558
  helix:  2.24 (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   0.010   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C  89 
 PHE   0.012   0.001   PHE D 118 
 TYR   0.005   0.001   TYR D 130 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  343)
  hydrogen bonds       : angle       4.03325 (  978)
  covalent geometry    : bond        0.00343 ( 4610)
  covalent geometry    : angle       0.57514 ( 6330)
  Misc. bond           : bond        0.08478 (    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: 7
    poor density    : 51
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A   76 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6711 (mtt)
REVERT: A   99 LYS cc_start: 0.8137 (mttm) cc_final: 0.7817 (mtmt)
REVERT: B   66 LYS cc_start: 0.7697 (mmmm) cc_final: 0.7188 (mttt)
REVERT: B   95 LYS cc_start: 0.7927 (tmtt) cc_final: 0.7356 (mptt)
REVERT: B  104 ARG cc_start: 0.7485 (ttp80) cc_final: 0.6273 (mpt180)
REVERT: C   61 LYS cc_start: 0.8075 (mttt) cc_final: 0.7632 (mtpt)
REVERT: C   76 MET cc_start: 0.7199 (mtt) cc_final: 0.6955 (mtt)
REVERT: C   99 LYS cc_start: 0.8133 (mttp) cc_final: 0.7836 (mtmt)
REVERT: D   66 LYS cc_start: 0.7754 (mmmm) cc_final: 0.7264 (mtmt)
REVERT: D   68 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7240 (mp)
REVERT: D   95 LYS cc_start: 0.7956 (tttt) cc_final: 0.7352 (mptt)
REVERT: D  104 ARG cc_start: 0.7440 (ttp80) cc_final: 0.6201 (mpt180)
REVERT: D  120 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6950 (tttp)
  outliers start: 7
  outliers final: 3
  residues processed: 55
  average time/residue: 1.6022
  time to fit residues: 90.7937
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 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 42 optimal weight:    0.4980
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4072 r_free = 0.4072 target = 0.188261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.166981 restraints weight = 3526.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 0.99
r_work: 0.3599 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2125

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= 0.150
  Angle     :  0.599   6.599   6330  Z= 0.281
  Chirality :  0.040   0.125    692
  Planarity :  0.005   0.048    790
  Dihedral  :  9.143  72.837    622
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.76 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.36), residues: 558
  helix:  2.13 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop : -0.04 (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   0.005   0.001   TYR D  35 
 ARG   0.002   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03890 (  343)
  hydrogen bonds       : angle       4.10668 (  978)
  covalent geometry    : bond        0.00392 ( 4610)
  covalent geometry    : angle       0.59913 ( 6330)
  Misc. bond           : bond        0.10837 (    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
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A   99 LYS cc_start: 0.8148 (mttm) cc_final: 0.7856 (mtmt)
REVERT: B   66 LYS cc_start: 0.7776 (mmmm) cc_final: 0.7264 (mttt)
REVERT: B   95 LYS cc_start: 0.7954 (tmtt) cc_final: 0.7434 (mptt)
REVERT: B  104 ARG cc_start: 0.7547 (ttp80) cc_final: 0.6377 (mpt180)
REVERT: C   61 LYS cc_start: 0.8096 (mttt) cc_final: 0.7675 (mtpt)
REVERT: C   76 MET cc_start: 0.7247 (mtt) cc_final: 0.7005 (mtt)
REVERT: C   99 LYS cc_start: 0.8154 (mttp) cc_final: 0.7899 (mtmt)
REVERT: D   66 LYS cc_start: 0.7797 (mmmm) cc_final: 0.7129 (mttt)
REVERT: D   68 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7212 (mp)
REVERT: D   95 LYS cc_start: 0.7976 (tttt) cc_final: 0.7439 (mptt)
REVERT: D  104 ARG cc_start: 0.7519 (ttp80) cc_final: 0.6329 (mpt180)
REVERT: D  120 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6964 (tttp)
  outliers start: 8
  outliers final: 4
  residues processed: 53
  average time/residue: 1.6251
  time to fit residues: 88.7856
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  : 0.478 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   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:    0.8580

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.172906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.153402 restraints weight = 3769.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 0.82
r_work: 0.3574 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.130   4614  Z= 0.168
  Angle     :  0.621   6.331   6330  Z= 0.292
  Chirality :  0.042   0.129    692
  Planarity :  0.006   0.048    790
  Dihedral  :  9.204  71.036    622
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.19
  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 (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:  2.33 (0.35), residues: 558
  helix:  2.01 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop : -0.04 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  14 
 HIS   0.005   0.001   HIS D 117 
 PHE   0.011   0.001   PHE B  85 
 TYR   0.005   0.001   TYR D 130 
 ARG   0.002   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 (  343)
  hydrogen bonds       : angle       4.19911 (  978)
  covalent geometry    : bond        0.00440 ( 4610)
  covalent geometry    : angle       0.62050 ( 6330)
  Misc. bond           : bond        0.11953 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3455.36 seconds
wall clock time: 60 minutes 21.20 seconds (3621.20 seconds total)