Starting phenix.real_space_refine
on Wed Sep 17 04:46:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqo_45817/09_2025/9cqo_45817.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqo_45817/09_2025/9cqo_45817.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqo_45817/09_2025/9cqo_45817.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqo_45817/09_2025/9cqo_45817.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqo_45817/09_2025/9cqo_45817.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqo_45817/09_2025/9cqo_45817.cif"
  }
  resolution = 3.01
  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=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      12      5.16       5
     C    2900      2.51       5
     N     760      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4470
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "C"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.58, per 1000 atoms: 0.35
  Number of scatterers: 4470
  At special positions: 0
  Unit cell: (76.44, 72.765, 66.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      12     16.00
     O     794      8.00
     N     760      7.00
     C    2900      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 189.4 milliseconds
  
  Enol-peptide restraints added in 715.3 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:
      39 helices and 0 sheets defined
      89.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  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: 3.607A  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: 3.766A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 4.182A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.057A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
    Processing helix  chain 'B' and resid 57 through 76
    Processing helix  chain 'B' and resid 77 through 79
      No H-bonds generated for 'chain 'B' and resid 77 through 79'
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.015A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.571A  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 90
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.690A  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: 3.657A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 35
      removed outlier: 3.905A  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: 3.568A  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 76
    Processing helix  chain 'D' and resid 77 through 79
      No H-bonds generated for 'chain 'D' and resid 77 through 79'
    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: 3.990A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.580A  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: 0.69

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 1647
        1.38 -     1.55: 2921
        1.55 -     1.72: 8
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4610
  Sorted by residual:
  bond pdb=" N   PHE D  42 "
       pdb=" CA  PHE D  42 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.18e-02 7.18e+03 1.03e+01
  bond pdb=" N   GLU D  43 "
       pdb=" CA  GLU D  43 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.21e-02 6.83e+03 9.34e+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 8.83e+00
  bond pdb=" N   HIS C  89 "
       pdb=" CA  HIS C  89 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.23e-02 6.61e+03 8.15e+00
  bond pdb=" N   VAL B 133 "
       pdb=" CA  VAL B 133 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.10e+00
  ... (remaining 4605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 5772
        1.22 -     2.43: 338
        2.43 -     3.65: 161
        3.65 -     4.87: 43
        4.87 -     6.09: 16
  Bond angle restraints: 6330
  Sorted by residual:
  angle pdb=" N   HIS C  89 "
        pdb=" CA  HIS C  89 "
        pdb=" C   HIS C  89 "
      ideal   model   delta    sigma   weight residual
     111.36  116.19   -4.83 1.09e+00 8.42e-01 1.96e+01
  angle pdb=" O   LEU A 113 "
        pdb=" C   LEU A 113 "
        pdb=" N   PRO A 114 "
      ideal   model   delta    sigma   weight residual
     121.37  117.45    3.92 9.00e-01 1.23e+00 1.90e+01
  angle pdb=" O   LEU C 113 "
        pdb=" C   LEU C 113 "
        pdb=" N   PRO C 114 "
      ideal   model   delta    sigma   weight residual
     121.37  117.52    3.85 9.00e-01 1.23e+00 1.83e+01
  angle pdb=" CA  HIS C  87 "
        pdb=" C   HIS C  87 "
        pdb=" O   HIS C  87 "
      ideal   model   delta    sigma   weight residual
     120.82  116.46    4.36 1.05e+00 9.07e-01 1.72e+01
  angle pdb=" CA  THR C 118 "
        pdb=" C   THR C 118 "
        pdb=" N   PRO C 119 "
      ideal   model   delta    sigma   weight residual
     117.48  122.07   -4.59 1.15e+00 7.56e-01 1.59e+01
  ... (remaining 6325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 2368
       17.73 -    35.46: 166
       35.46 -    53.19: 56
       53.19 -    70.93: 15
       70.93 -    88.66: 9
  Dihedral angle restraints: 2614
    sinusoidal: 990
      harmonic: 1624
  Sorted by residual:
  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  -83.44   83.44     2      2.00e+01 2.50e-03 1.18e+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  -75.84   75.84     2      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" C2D HEM C 201 "
           pdb=" C3D HEM C 201 "
           pdb=" CAD HEM C 201 "
           pdb=" CBD HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -107.83  -72.17     2      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 2611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 564
       0.055 -    0.110: 99
       0.110 -    0.164: 20
       0.164 -    0.219: 6
       0.219 -    0.274: 3
  Chirality restraints: 692
  Sorted by residual:
  chirality pdb=" CB  VAL B 134 "
            pdb=" CA  VAL B 134 "
            pdb=" CG1 VAL B 134 "
            pdb=" CG2 VAL B 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.87e+00
  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   -2.36   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  HIS C  89 "
            pdb=" N   HIS C  89 "
            pdb=" C   HIS C  89 "
            pdb=" CB  HIS C  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 689 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A   3 "    0.036 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO A   4 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A   4 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A   4 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 113 "    0.011 2.00e-02 2.50e+03   2.06e-02 4.25e+00
        pdb=" C   LEU A 113 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   LEU A 113 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PRO A 114 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 123 "    0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO B 124 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "    0.025 5.00e-02 4.00e+02
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 599
        2.75 -     3.29: 4268
        3.29 -     3.83: 7836
        3.83 -     4.36: 8979
        4.36 -     4.90: 15757
  Nonbonded interactions: 37439
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  27 "
            pdb=" NE2 HIS A 112 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OE1 GLU C  27 "
            pdb=" NE2 HIS C 112 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OE1 GLU D  26 "
            pdb=" NE2 HIS D 117 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" O   PRO A  77 "
            pdb=" OH  TYR A 140 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   SER A 133 "
            pdb=" OG1 THR A 137 "
     model   vdw
     2.305 3.040
  ... (remaining 37434 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:             4.510
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.730
  Find NCS groups from input model:        0.100
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
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      :  0.007   0.225   4614  Z= 0.339
  Angle     :  0.837   6.087   6330  Z= 0.564
  Chirality :  0.050   0.274    692
  Planarity :  0.006   0.055    790
  Dihedral  : 15.651  88.657   1562
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 10.79 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.00 (0.36), residues: 558
  helix:  2.39 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.58 (0.62), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  92 
 TYR   0.006   0.001   TYR B  35 
 PHE   0.013   0.002   PHE D  42 
 TRP   0.013   0.002   TRP D  15 
 HIS   0.005   0.001   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 4610)
  covalent geometry    : angle       0.83665 ( 6330)
  hydrogen bonds       : bond        0.11535 (  343)
  hydrogen bonds       : angle       4.90656 (  978)
  Misc. bond           : bond        0.17153 (    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
  61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.7942 (tptp) cc_final: 0.7455 (ttmm)
REVERT: A   61 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7676 (mtpt)
REVERT: A   92 ARG cc_start: 0.8636 (mtt-85) cc_final: 0.7604 (mtm-85)
REVERT: B   52 ASP cc_start: 0.8214 (m-30) cc_final: 0.8006 (m-30)
REVERT: B   65 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8160 (tttt)
  outliers start: 13
  outliers final: 4
  residues processed: 58
  average time/residue: 0.1181
  time to fit residues: 8.1020
Evaluate side-chains
  46 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 131 GLN
C  89 HIS
D  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.155375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.129397 restraints weight = 4245.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.32
r_work: 0.3205 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107   4614  Z= 0.157
  Angle     :  0.597   5.379   6330  Z= 0.281
  Chirality :  0.040   0.127    692
  Planarity :  0.006   0.047    790
  Dihedral  : 10.202  85.101    624
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  9.25 %
    Favored  : 87.67 %
  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:  2.84 (0.36), residues: 558
  helix:  2.27 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.54 (0.61), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  92 
 TYR   0.008   0.001   TYR A  42 
 PHE   0.012   0.002   PHE D  85 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.005   0.001   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 4610)
  covalent geometry    : angle       0.59705 ( 6330)
  hydrogen bonds       : bond        0.04077 (  343)
  hydrogen bonds       : angle       4.15276 (  978)
  Misc. bond           : bond        0.09741 (    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: 14
    poor density    : 46
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.7891 (tptp) cc_final: 0.7280 (ttmm)
REVERT: A   61 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7337 (mtpt)
REVERT: A   92 ARG cc_start: 0.8740 (mtt-85) cc_final: 0.7721 (mtm-85)
REVERT: B   65 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7808 (tttm)
REVERT: C   76 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6894 (mtt)
REVERT: D   43 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6178 (pm20)
REVERT: D  120 LYS cc_start: 0.7537 (mmtp) cc_final: 0.7153 (mmmt)
  outliers start: 14
  outliers final: 8
  residues processed: 54
  average time/residue: 0.1142
  time to fit residues: 7.4735
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue   89 SER
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 22 optimal weight:    0.4980
   chunk 35 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 46 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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.158306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.133189 restraints weight = 4203.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.24
r_work: 0.3222 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.128   4614  Z= 0.140
  Angle     :  0.576   5.952   6330  Z= 0.264
  Chirality :  0.039   0.123    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.962  83.132    624
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  :  7.49 %
    Favored  : 89.21 %
  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:  2.88 (0.36), residues: 558
  helix:  2.31 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.52 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  92 
 TYR   0.005   0.001   TYR A  42 
 PHE   0.008   0.001   PHE D  85 
 TRP   0.009   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 4610)
  covalent geometry    : angle       0.57619 ( 6330)
  hydrogen bonds       : bond        0.03622 (  343)
  hydrogen bonds       : angle       4.03202 (  978)
  Misc. bond           : bond        0.09457 (    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
  60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LYS cc_start: 0.7883 (tptp) cc_final: 0.7260 (ttmm)
REVERT: A   61 LYS cc_start: 0.7821 (mtpp) cc_final: 0.7263 (mtpt)
REVERT: A   76 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6601 (mmt)
REVERT: A   92 ARG cc_start: 0.8744 (mtt-85) cc_final: 0.7760 (mtm-85)
REVERT: B   66 LYS cc_start: 0.8172 (mmmm) cc_final: 0.7525 (mtpt)
REVERT: B  120 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7179 (tttt)
REVERT: C   76 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6787 (mtt)
REVERT: D  120 LYS cc_start: 0.7537 (mmtp) cc_final: 0.7170 (mmmt)
  outliers start: 15
  outliers final: 8
  residues processed: 52
  average time/residue: 0.1040
  time to fit residues: 6.5556
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.156711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.135101 restraints weight = 4203.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 0.94
r_work: 0.3222 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.161   4614  Z= 0.153
  Angle     :  0.588   6.069   6330  Z= 0.270
  Chirality :  0.040   0.123    692
  Planarity :  0.005   0.048    790
  Dihedral  :  9.961  82.862    622
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  :  8.59 %
    Favored  : 88.11 %
  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:  2.78 (0.36), residues: 558
  helix:  2.26 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.38 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  92 
 TYR   0.006   0.001   TYR A  42 
 PHE   0.010   0.001   PHE D  85 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.007   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 4610)
  covalent geometry    : angle       0.58846 ( 6330)
  hydrogen bonds       : bond        0.03826 (  343)
  hydrogen bonds       : angle       4.05652 (  978)
  Misc. bond           : bond        0.11065 (    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
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8125 (tptp) cc_final: 0.7600 (ttmm)
REVERT: A   61 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7578 (mtpt)
REVERT: A   92 ARG cc_start: 0.8713 (mtt-85) cc_final: 0.7888 (mtm-85)
REVERT: B   66 LYS cc_start: 0.8420 (mmmm) cc_final: 0.7831 (mtpt)
REVERT: B  120 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7341 (tttt)
REVERT: C   60 LYS cc_start: 0.8046 (tptp) cc_final: 0.7384 (tppt)
REVERT: C   76 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6867 (mtt)
REVERT: D   43 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6464 (pm20)
REVERT: D  120 LYS cc_start: 0.7558 (mmtp) cc_final: 0.7260 (mmmt)
  outliers start: 15
  outliers final: 11
  residues processed: 51
  average time/residue: 0.1197
  time to fit residues: 7.3079
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   78 LEU
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:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0020
   overall best weight:    0.6188

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.157369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.135904 restraints weight = 4207.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 0.94
r_work: 0.3234 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.142   4614  Z= 0.135
  Angle     :  0.572   6.495   6330  Z= 0.260
  Chirality :  0.038   0.123    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.886  82.550    622
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  :  9.25 %
    Favored  : 87.89 %
  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:  2.88 (0.36), residues: 558
  helix:  2.35 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.34 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  92 
 TYR   0.005   0.001   TYR B  35 
 PHE   0.007   0.001   PHE C  43 
 TRP   0.010   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4610)
  covalent geometry    : angle       0.57161 ( 6330)
  hydrogen bonds       : bond        0.03537 (  343)
  hydrogen bonds       : angle       3.99372 (  978)
  Misc. bond           : bond        0.09613 (    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
  56 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8130 (tptp) cc_final: 0.7601 (ttmm)
REVERT: A   61 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7576 (mtpt)
REVERT: A   76 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6785 (mmt)
REVERT: A   92 ARG cc_start: 0.8711 (mtt-85) cc_final: 0.7861 (mtm-85)
REVERT: B   26 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7422 (mm-30)
REVERT: B   66 LYS cc_start: 0.8391 (mmmm) cc_final: 0.7824 (mtpt)
REVERT: C   60 LYS cc_start: 0.8024 (tptp) cc_final: 0.7354 (tppt)
REVERT: C   76 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6818 (mtt)
REVERT: D   43 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6532 (pm20)
REVERT: D  120 LYS cc_start: 0.7537 (mmtp) cc_final: 0.7237 (mmmt)
  outliers start: 13
  outliers final: 8
  residues processed: 49
  average time/residue: 0.1210
  time to fit residues: 7.0668
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
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:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0020
   chunk 34 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6388

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.157077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.134753 restraints weight = 4251.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 0.99
r_work: 0.3222 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.140   4614  Z= 0.136
  Angle     :  0.570   6.443   6330  Z= 0.259
  Chirality :  0.039   0.122    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.723  82.909    620
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  :  8.59 %
    Favored  : 87.67 %
  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:  2.90 (0.36), residues: 558
  helix:  2.36 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.33 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  92 
 TYR   0.005   0.001   TYR A  42 
 PHE   0.007   0.001   PHE D  85 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.005   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4610)
  covalent geometry    : angle       0.57019 ( 6330)
  hydrogen bonds       : bond        0.03532 (  343)
  hydrogen bonds       : angle       3.98519 (  978)
  Misc. bond           : bond        0.09627 (    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: 17
    poor density    : 42
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8137 (tptp) cc_final: 0.7595 (ttmm)
REVERT: A   61 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7573 (mtpt)
REVERT: A   76 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6738 (mmt)
REVERT: A   92 ARG cc_start: 0.8718 (mtt-85) cc_final: 0.7864 (mtm-85)
REVERT: B   26 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7448 (mm-30)
REVERT: B   66 LYS cc_start: 0.8388 (mmmm) cc_final: 0.7823 (mtpt)
REVERT: B  120 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7343 (tttt)
REVERT: C   60 LYS cc_start: 0.8031 (tptp) cc_final: 0.7349 (tppt)
REVERT: C   76 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6852 (mtt)
REVERT: D   43 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6675 (pm20)
REVERT: D  120 LYS cc_start: 0.7550 (mmtp) cc_final: 0.7212 (mmmt)
  outliers start: 17
  outliers final: 10
  residues processed: 52
  average time/residue: 0.1022
  time to fit residues: 6.5019
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.155050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.130048 restraints weight = 4300.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.23
r_work: 0.3192 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.147   4614  Z= 0.165
  Angle     :  0.595   6.765   6330  Z= 0.273
  Chirality :  0.040   0.126    692
  Planarity :  0.005   0.048    790
  Dihedral  :  9.796  84.046    620
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  :  9.69 %
    Favored  : 86.78 %
  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:  2.73 (0.36), residues: 558
  helix:  2.24 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.26 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  92 
 TYR   0.006   0.001   TYR A  42 
 PHE   0.010   0.001   PHE D  85 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.004   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 4610)
  covalent geometry    : angle       0.59518 ( 6330)
  hydrogen bonds       : bond        0.03900 (  343)
  hydrogen bonds       : angle       4.09729 (  978)
  Misc. bond           : bond        0.10865 (    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
  58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.7981 (tptp) cc_final: 0.7338 (ttmm)
REVERT: A   61 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7338 (mtpt)
REVERT: A   92 ARG cc_start: 0.8752 (mtt-85) cc_final: 0.7775 (mtm-85)
REVERT: B    8 LYS cc_start: 0.7366 (tppt) cc_final: 0.6913 (mttm)
REVERT: B   26 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7207 (mt-10)
REVERT: B   66 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7553 (mtpt)
REVERT: B  120 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7233 (tttt)
REVERT: C   60 LYS cc_start: 0.7938 (tptp) cc_final: 0.7075 (ttmm)
REVERT: C   76 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6874 (mtt)
  outliers start: 16
  outliers final: 12
  residues processed: 51
  average time/residue: 0.1129
  time to fit residues: 6.9059
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
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:    7.9990
   chunk 40 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 19 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0980
   overall best weight:    0.5580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.157088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.135722 restraints weight = 4239.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 0.93
r_work: 0.3241 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.137   4614  Z= 0.129
  Angle     :  0.564   6.367   6330  Z= 0.256
  Chirality :  0.038   0.121    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.688  83.008    620
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  :  9.91 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.89 (0.36), residues: 558
  helix:  2.38 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.25 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  92 
 TYR   0.005   0.001   TYR A  42 
 PHE   0.007   0.001   PHE C  43 
 TRP   0.011   0.001   TRP C  14 
 HIS   0.005   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4610)
  covalent geometry    : angle       0.56419 ( 6330)
  hydrogen bonds       : bond        0.03410 (  343)
  hydrogen bonds       : angle       3.98722 (  978)
  Misc. bond           : bond        0.09231 (    4)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8164 (tptp) cc_final: 0.7637 (ttmm)
REVERT: A   61 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7572 (mtpt)
REVERT: A   76 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6795 (mmt)
REVERT: A   92 ARG cc_start: 0.8697 (mtt-85) cc_final: 0.7871 (mtm-85)
REVERT: B    8 LYS cc_start: 0.7627 (tppt) cc_final: 0.7177 (mttm)
REVERT: B   26 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7405 (mm-30)
REVERT: B   66 LYS cc_start: 0.8393 (mmmm) cc_final: 0.7846 (mtpt)
REVERT: B  120 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7345 (tttt)
REVERT: C   60 LYS cc_start: 0.8077 (tptp) cc_final: 0.7412 (tppt)
REVERT: C   76 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6856 (mtt)
REVERT: D   43 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6862 (pm20)
REVERT: D  120 LYS cc_start: 0.7425 (mmtm) cc_final: 0.7168 (mmmt)
  outliers start: 16
  outliers final: 9
  residues processed: 49
  average time/residue: 0.1180
  time to fit residues: 6.8635
Evaluate side-chains
  54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
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:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0970
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7178

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.156053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.134748 restraints weight = 4214.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 0.93
r_work: 0.3231 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
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      :  0.005   0.142   4614  Z= 0.145
  Angle     :  0.578   6.565   6330  Z= 0.265
  Chirality :  0.039   0.147    692
  Planarity :  0.005   0.047    790
  Dihedral  :  9.732  83.902    620
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 10.35 %
    Favored  : 86.34 %
  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:  2.82 (0.36), residues: 558
  helix:  2.32 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.22 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  92 
 TYR   0.006   0.001   TYR A  42 
 PHE   0.008   0.001   PHE D  85 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.005   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 4610)
  covalent geometry    : angle       0.57827 ( 6330)
  hydrogen bonds       : bond        0.03644 (  343)
  hydrogen bonds       : angle       4.03816 (  978)
  Misc. bond           : bond        0.10041 (    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
  56 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8148 (tptp) cc_final: 0.7609 (ttmm)
REVERT: A   61 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7583 (mtpt)
REVERT: A   92 ARG cc_start: 0.8698 (mtt-85) cc_final: 0.7862 (mtm-85)
REVERT: B    8 LYS cc_start: 0.7644 (tppt) cc_final: 0.7190 (mttm)
REVERT: B   26 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7409 (mm-30)
REVERT: B   66 LYS cc_start: 0.8413 (mmmm) cc_final: 0.7859 (mtpt)
REVERT: B  120 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7351 (tttt)
REVERT: C   60 LYS cc_start: 0.8111 (tptp) cc_final: 0.7434 (tppt)
REVERT: C   76 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6865 (mtt)
REVERT: D  120 LYS cc_start: 0.7481 (mmtm) cc_final: 0.7169 (mmmt)
  outliers start: 15
  outliers final: 12
  residues processed: 49
  average time/residue: 0.0992
  time to fit residues: 5.9022
Evaluate side-chains
  56 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   78 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 43 optimal weight:    0.2980
   chunk 39 optimal weight:    0.0980
   chunk 4 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 45 optimal weight:    0.3980
   chunk 44 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
B 102 ASN
C  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.158361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.136233 restraints weight = 4211.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 0.97
r_work: 0.3242 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.129   4614  Z= 0.113
  Angle     :  0.548   6.058   6330  Z= 0.248
  Chirality :  0.037   0.141    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.622  82.795    620
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  :  9.91 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.05 (0.36), residues: 558
  helix:  2.52 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.20 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  92 
 TYR   0.005   0.001   TYR A  42 
 PHE   0.006   0.001   PHE C  43 
 TRP   0.010   0.001   TRP C  14 
 HIS   0.005   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4610)
  covalent geometry    : angle       0.54777 ( 6330)
  hydrogen bonds       : bond        0.03133 (  343)
  hydrogen bonds       : angle       3.92936 (  978)
  Misc. bond           : bond        0.08280 (    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
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8109 (tptp) cc_final: 0.7567 (ttmm)
REVERT: A   61 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7544 (mtpt)
REVERT: A   76 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6774 (mmt)
REVERT: A   92 ARG cc_start: 0.8709 (mtt-85) cc_final: 0.7858 (mtm-85)
REVERT: B    8 LYS cc_start: 0.7558 (tppt) cc_final: 0.7175 (mttm)
REVERT: B   26 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7435 (mm-30)
REVERT: B   66 LYS cc_start: 0.8361 (mmmm) cc_final: 0.7819 (mtpt)
REVERT: B  120 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7348 (tttt)
REVERT: C   60 LYS cc_start: 0.8011 (tptp) cc_final: 0.7324 (tppt)
REVERT: C   76 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6909 (mtt)
REVERT: D   43 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6916 (pm20)
REVERT: D  120 LYS cc_start: 0.7457 (mmtm) cc_final: 0.7156 (mmmt)
  outliers start: 16
  outliers final: 9
  residues processed: 49
  average time/residue: 0.1051
  time to fit residues: 6.2881
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   76 MET
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   76 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   78 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:    0.0570
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0030
   chunk 6 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.3708

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.159342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.137263 restraints weight = 4186.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 0.96
r_work: 0.3255 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.126   4614  Z= 0.110
  Angle     :  0.542   5.933   6330  Z= 0.244
  Chirality :  0.038   0.145    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.591  82.842    620
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 10.35 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.19 (0.36), residues: 558
  helix:  2.63 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.21 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  92 
 TYR   0.006   0.001   TYR A  42 
 PHE   0.005   0.001   PHE C  43 
 TRP   0.011   0.001   TRP C  14 
 HIS   0.005   0.001   HIS C  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4610)
  covalent geometry    : angle       0.54201 ( 6330)
  hydrogen bonds       : bond        0.03041 (  343)
  hydrogen bonds       : angle       3.87862 (  978)
  Misc. bond           : bond        0.08096 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1352.12 seconds
wall clock time: 23 minutes 55.10 seconds (1435.10 seconds total)