Starting phenix.real_space_refine
on Wed Jun  4 23:12:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqv_45824/06_2025/9cqv_45824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqv_45824/06_2025/9cqv_45824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqv_45824/06_2025/9cqv_45824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqv_45824/06_2025/9cqv_45824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqv_45824/06_2025/9cqv_45824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqv_45824/06_2025/9cqv_45824.cif"
  }
  resolution = 2.75
  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=   0.020
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 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4470
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "C"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.24, per 1000 atoms: 0.95
  Number of scatterers: 4470
  At special positions: 0
  Unit cell: (81.585, 72.765, 66.885, 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: 1.35
  Conformation dependent library (CDL) restraints added in 589.0 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:
      37 helices and 0 sheets defined
      87.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  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 90
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.554A  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 16
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 3.512A  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
      removed outlier: 3.990A  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 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.031A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.592A  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: 3.670A  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: 3.866A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 35
      removed outlier: 3.635A  pdb=" N   GLY D  24 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 3.642A  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 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: 3.982A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.660A  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

    341 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: 1.14

  Time building geometry restraints manager: 1.59 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: 1629
        1.38 -     1.55: 2938
        1.55 -     1.72: 9
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4610
  Sorted by residual:
  bond pdb=" N   VAL B  23 "
       pdb=" CA  VAL B  23 "
    ideal  model  delta    sigma   weight residual
    1.460  1.500 -0.041 1.21e-02 6.83e+03 1.13e+01
  bond pdb=" N   VAL D  23 "
       pdb=" CA  VAL D  23 "
    ideal  model  delta    sigma   weight residual
    1.460  1.499 -0.040 1.21e-02 6.83e+03 1.07e+01
  bond pdb=" N   VAL B  18 "
       pdb=" CA  VAL B  18 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.20e-02 6.94e+03 8.75e+00
  bond pdb=" N   ASN B  80 "
       pdb=" CA  ASN B  80 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.16e-02 7.43e+03 8.45e+00
  bond pdb=" N   THR C  38 "
       pdb=" CA  THR C  38 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.21e-02 6.83e+03 8.43e+00
  ... (remaining 4605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 5880
        1.36 -     2.72: 308
        2.72 -     4.08: 110
        4.08 -     5.44: 29
        5.44 -     6.80: 3
  Bond angle restraints: 6330
  Sorted by residual:
  angle pdb=" C   PHE C  36 "
        pdb=" N   PRO C  37 "
        pdb=" CA  PRO C  37 "
      ideal   model   delta    sigma   weight residual
     118.85  124.27   -5.42 1.09e+00 8.42e-01 2.47e+01
  angle pdb=" CA  LEU B  81 "
        pdb=" C   LEU B  81 "
        pdb=" O   LEU B  81 "
      ideal   model   delta    sigma   weight residual
     120.55  116.25    4.30 1.06e+00 8.90e-01 1.65e+01
  angle pdb=" N   GLU D  22 "
        pdb=" CA  GLU D  22 "
        pdb=" C   GLU D  22 "
      ideal   model   delta    sigma   weight residual
     111.14  115.07   -3.93 1.08e+00 8.57e-01 1.33e+01
  angle pdb=" N   VAL D 137 "
        pdb=" CA  VAL D 137 "
        pdb=" C   VAL D 137 "
      ideal   model   delta    sigma   weight residual
     110.72  107.25    3.47 1.01e+00 9.80e-01 1.18e+01
  angle pdb=" CA  LYS C  40 "
        pdb=" C   LYS C  40 "
        pdb=" O   LYS C  40 "
      ideal   model   delta    sigma   weight residual
     120.55  116.97    3.58 1.06e+00 8.90e-01 1.14e+01
  ... (remaining 6325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 2257
       15.99 -    31.98: 227
       31.98 -    47.97: 93
       47.97 -    63.96: 29
       63.96 -    79.95: 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  -39.81  -50.19     2      1.50e+01 4.44e-03 1.26e+01
  dihedral pdb=" C2D HEM A 201 "
           pdb=" C3D HEM A 201 "
           pdb=" CAD HEM A 201 "
           pdb=" CBD HEM A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -100.05  -79.95     2      2.00e+01 2.50e-03 1.16e+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  -78.97   78.97     2      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 2611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 560
       0.058 -    0.116: 100
       0.116 -    0.175: 25
       0.175 -    0.233: 5
       0.233 -    0.291: 2
  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   -2.34   -0.29 2.00e-01 2.50e+01 2.12e+00
  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   -2.37   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  VAL B  18 "
            pdb=" CA  VAL B  18 "
            pdb=" CG1 VAL B  18 "
            pdb=" CG2 VAL B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 689 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C  40 "   -0.009 2.00e-02 2.50e+03   1.90e-02 3.60e+00
        pdb=" C   LYS C  40 "    0.033 2.00e-02 2.50e+03
        pdb=" O   LYS C  40 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   THR C  41 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  99 "   -0.030 5.00e-02 4.00e+02   4.48e-02 3.21e+00
        pdb=" N   PRO B 100 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 100 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 100 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 123 "    0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO B 124 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "    0.024 5.00e-02 4.00e+02
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 419
        2.74 -     3.28: 4311
        3.28 -     3.82: 7885
        3.82 -     4.36: 9191
        4.36 -     4.90: 15788
  Nonbonded interactions: 37594
  Sorted by model distance:
  nonbonded pdb=" OG  SER C   3 "
            pdb=" OD1 ASP C   6 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OE1 GLU D 101 "
            pdb=" NH1 ARG D 104 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" OE1 GLU B 101 "
            pdb=" NH1 ARG B 104 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" O   PRO A 114 "
            pdb=" NE2 HIS B 116 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" OE1 GLU C  27 "
            pdb=" NE2 HIS C 112 "
     model   vdw
     2.379 3.120
  ... (remaining 37589 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:             2.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.130
  Find NCS groups from input model:        0.170
  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:13.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
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   0.165   4614  Z= 0.332
  Angle     :  0.790   6.804   6330  Z= 0.516
  Chirality :  0.052   0.291    692
  Planarity :  0.006   0.045    790
  Dihedral  : 16.702  79.948   1562
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.74 %
    Favored  : 80.18 %
  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:  2.90 (0.35), residues: 558
  helix:  2.48 (0.24), residues: 434
  sheet:  None (None), residues: 0
  loop : -0.13 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  14 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.015   0.001   PHE C  36 
 TYR   0.009   0.002   TYR A  24 
 ARG   0.008   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12235 (  341)
  hydrogen bonds       : angle       4.89783 (  978)
  covalent geometry    : bond        0.00508 ( 4610)
  covalent geometry    : angle       0.79010 ( 6330)
  Misc. bond           : bond        0.10715 (    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
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A  139 LYS cc_start: 0.4413 (OUTLIER) cc_final: 0.3384 (ptpt)
REVERT: A  140 TYR cc_start: -0.0282 (OUTLIER) cc_final: -0.0601 (m-80)
REVERT: D   17 LYS cc_start: 0.8177 (mptp) cc_final: 0.7810 (mtpt)
REVERT: D   90 GLU cc_start: 0.7980 (tt0) cc_final: 0.7328 (tp30)
  outliers start: 14
  outliers final: 5
  residues processed: 72
  average time/residue: 1.5796
  time to fit residues: 117.5016
Evaluate side-chains
  65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
B 131 GLN
C  68 ASN
D  19 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.147201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.127231 restraints weight = 4523.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.63
r_work: 0.3422 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.0886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.092   4614  Z= 0.150
  Angle     :  0.596   7.049   6330  Z= 0.279
  Chirality :  0.040   0.130    692
  Planarity :  0.006   0.045    790
  Dihedral  : 10.369  81.753    630
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 13.22 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.96 (0.35), residues: 558
  helix:  2.41 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.33 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.005   0.001   HIS B  63 
 PHE   0.012   0.002   PHE B 118 
 TYR   0.008   0.002   TYR B  35 
 ARG   0.007   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  341)
  hydrogen bonds       : angle       4.08761 (  978)
  covalent geometry    : bond        0.00399 ( 4610)
  covalent geometry    : angle       0.59629 ( 6330)
  Misc. bond           : bond        0.07247 (    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
  86 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7810 (tptp) cc_final: 0.7280 (mptt)
REVERT: B   95 LYS cc_start: 0.7774 (tttt) cc_final: 0.7293 (mptt)
REVERT: D   17 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7968 (mtpt)
REVERT: D   32 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8701 (mp)
REVERT: D   66 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7991 (mtmm)
REVERT: D   82 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7456 (tttt)
REVERT: D   90 GLU cc_start: 0.7959 (tt0) cc_final: 0.7290 (tp30)
REVERT: D  134 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.7389 (m)
  outliers start: 22
  outliers final: 10
  residues processed: 77
  average time/residue: 1.9719
  time to fit residues: 157.6418
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0570
   chunk 31 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
B 131 GLN
C  68 ASN
D  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.146909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.126982 restraints weight = 4516.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.63
r_work: 0.3421 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   4614  Z= 0.139
  Angle     :  0.580   6.606   6330  Z= 0.269
  Chirality :  0.040   0.125    692
  Planarity :  0.006   0.045    790
  Dihedral  : 10.112  81.275    624
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 14.76 %
    Favored  : 80.40 %
  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:  2.97 (0.35), residues: 558
  helix:  2.44 (0.24), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.28 (0.57), 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  58 
 PHE   0.010   0.001   PHE B 118 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.006   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03767 (  341)
  hydrogen bonds       : angle       3.95923 (  978)
  covalent geometry    : bond        0.00374 ( 4610)
  covalent geometry    : angle       0.57962 ( 6330)
  Misc. bond           : bond        0.07195 (    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
  84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.534 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7827 (tptp) cc_final: 0.7314 (mptt)
REVERT: B   95 LYS cc_start: 0.7698 (tttt) cc_final: 0.7352 (mptt)
REVERT: D   17 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8025 (mtpt)
REVERT: D   66 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7977 (mtmm)
REVERT: D   82 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7439 (tttt)
REVERT: D   90 GLU cc_start: 0.7949 (tt0) cc_final: 0.7286 (tp30)
REVERT: D  134 VAL cc_start: 0.7595 (OUTLIER) cc_final: 0.7346 (m)
  outliers start: 22
  outliers final: 11
  residues processed: 74
  average time/residue: 1.6981
  time to fit residues: 129.5714
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 49 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0040
   chunk 37 optimal weight:    0.3980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
B  80 ASN
B 117 HIS
C   9 ASN
D  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.149101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.129178 restraints weight = 4521.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.64
r_work: 0.3453 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   4614  Z= 0.113
  Angle     :  0.546   5.743   6330  Z= 0.250
  Chirality :  0.038   0.153    692
  Planarity :  0.005   0.044    790
  Dihedral  :  9.771  79.698    624
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 15.86 %
    Favored  : 80.18 %
  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:  3.21 (0.36), residues: 558
  helix:  2.61 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.30 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C  58 
 PHE   0.007   0.001   PHE B 118 
 TYR   0.006   0.001   TYR B  35 
 ARG   0.006   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03139 (  341)
  hydrogen bonds       : angle       3.76855 (  978)
  covalent geometry    : bond        0.00308 ( 4610)
  covalent geometry    : angle       0.54572 ( 6330)
  Misc. bond           : bond        0.05809 (    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
  79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.513 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7848 (tptp) cc_final: 0.7368 (mptt)
REVERT: B   26 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7407 (mm-30)
REVERT: B   90 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6786 (mt-10)
REVERT: B   95 LYS cc_start: 0.7636 (tttt) cc_final: 0.7393 (mptt)
REVERT: D   17 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7954 (mtpt)
REVERT: D   66 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7902 (mtmm)
REVERT: D   82 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7444 (tttt)
REVERT: D   90 GLU cc_start: 0.7904 (tt0) cc_final: 0.7299 (tm-30)
REVERT: D  134 VAL cc_start: 0.7477 (OUTLIER) cc_final: 0.7256 (m)
  outliers start: 18
  outliers final: 6
  residues processed: 71
  average time/residue: 1.8341
  time to fit residues: 134.1782
Evaluate side-chains
  69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 TYR
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   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 1 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 28 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.147341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.127298 restraints weight = 4583.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.65
r_work: 0.3425 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   4614  Z= 0.129
  Angle     :  0.567   6.473   6330  Z= 0.261
  Chirality :  0.039   0.124    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.722  81.366    622
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 15.42 %
    Favored  : 80.84 %
  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:  3.14 (0.36), residues: 558
  helix:  2.58 (0.24), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.27 (0.57), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 
 PHE   0.009   0.001   PHE B 118 
 TYR   0.007   0.001   TYR B  35 
 ARG   0.006   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  341)
  hydrogen bonds       : angle       3.81905 (  978)
  covalent geometry    : bond        0.00350 ( 4610)
  covalent geometry    : angle       0.56742 ( 6330)
  Misc. bond           : bond        0.07227 (    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
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7875 (tptp) cc_final: 0.7450 (mptt)
REVERT: B   21 ASP cc_start: 0.6207 (OUTLIER) cc_final: 0.5872 (m-30)
REVERT: B   26 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7385 (mm-30)
REVERT: B   90 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6831 (mt-10)
REVERT: B   95 LYS cc_start: 0.7686 (tttt) cc_final: 0.7448 (mptt)
REVERT: D   17 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8021 (mtpt)
REVERT: D   66 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7958 (mtmm)
REVERT: D   82 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7365 (tppt)
REVERT: D   90 GLU cc_start: 0.7899 (tt0) cc_final: 0.7292 (tm-30)
REVERT: D  134 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7297 (m)
  outliers start: 17
  outliers final: 7
  residues processed: 72
  average time/residue: 1.8227
  time to fit residues: 135.2258
Evaluate side-chains
  73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 TYR
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   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 49 optimal weight:    0.3980
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0980
   chunk 35 optimal weight:    0.4980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.149416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.130003 restraints weight = 4518.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.59
r_work: 0.3446 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   4614  Z= 0.114
  Angle     :  0.550   5.877   6330  Z= 0.252
  Chirality :  0.038   0.122    692
  Planarity :  0.005   0.044    790
  Dihedral  :  9.619  80.989    622
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 14.98 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.30 (0.36), residues: 558
  helix:  2.58 (0.24), residues: 446
  sheet:  None (None), residues: 0
  loop :  0.58 (0.63), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C  58 
 PHE   0.007   0.001   PHE B 118 
 TYR   0.006   0.001   TYR B  35 
 ARG   0.006   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03182 (  341)
  hydrogen bonds       : angle       3.72903 (  978)
  covalent geometry    : bond        0.00310 ( 4610)
  covalent geometry    : angle       0.54997 ( 6330)
  Misc. bond           : bond        0.06235 (    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
  78 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7860 (tptp) cc_final: 0.7450 (mptt)
REVERT: B   21 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5806 (m-30)
REVERT: B   26 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7399 (mm-30)
REVERT: B   90 GLU cc_start: 0.7494 (tm-30) cc_final: 0.6841 (mt-10)
REVERT: B  101 GLU cc_start: 0.7834 (tp30) cc_final: 0.7604 (tp30)
REVERT: D   17 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7994 (mtpt)
REVERT: D   66 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7943 (mtmm)
REVERT: D   82 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7354 (tppt)
REVERT: D   90 GLU cc_start: 0.7896 (tt0) cc_final: 0.7314 (tm-30)
REVERT: D  134 VAL cc_start: 0.7570 (OUTLIER) cc_final: 0.7322 (m)
  outliers start: 18
  outliers final: 4
  residues processed: 70
  average time/residue: 1.4347
  time to fit residues: 103.7584
Evaluate side-chains
  68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
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   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0270
   overall best weight:    0.9442

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.145456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.125443 restraints weight = 4531.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.63
r_work: 0.3412 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.100   4614  Z= 0.161
  Angle     :  0.610   7.342   6330  Z= 0.284
  Chirality :  0.042   0.147    692
  Planarity :  0.006   0.046    790
  Dihedral  :  9.733  83.884    620
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.64 %
    Favored  : 80.84 %
  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:  3.00 (0.36), residues: 558
  helix:  2.36 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.53 (0.59), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  14 
 HIS   0.005   0.001   HIS B  63 
 PHE   0.011   0.001   PHE B 118 
 TYR   0.007   0.001   TYR B  35 
 ARG   0.007   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  341)
  hydrogen bonds       : angle       3.92528 (  978)
  covalent geometry    : bond        0.00432 ( 4610)
  covalent geometry    : angle       0.60992 ( 6330)
  Misc. bond           : bond        0.08207 (    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
  78 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7918 (tptp) cc_final: 0.7561 (mptt)
REVERT: B   26 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7411 (mm-30)
REVERT: C   56 LYS cc_start: 0.7966 (tttt) cc_final: 0.7460 (mptt)
REVERT: D   17 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8036 (mtpt)
REVERT: D   66 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8017 (mtmm)
REVERT: D   82 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7355 (tppt)
REVERT: D   90 GLU cc_start: 0.7920 (tt0) cc_final: 0.7291 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 71
  average time/residue: 1.4546
  time to fit residues: 106.6106
Evaluate side-chains
  75 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.145661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.125809 restraints weight = 4470.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.62
r_work: 0.3417 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088   4614  Z= 0.153
  Angle     :  0.605   7.019   6330  Z= 0.280
  Chirality :  0.041   0.127    692
  Planarity :  0.006   0.047    790
  Dihedral  :  9.753  83.449    620
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 15.86 %
    Favored  : 80.40 %
  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:  2.98 (0.35), residues: 558
  helix:  2.34 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.58 (0.60), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 
 PHE   0.010   0.001   PHE B 118 
 TYR   0.007   0.001   TYR B  35 
 ARG   0.007   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03928 (  341)
  hydrogen bonds       : angle       3.91776 (  978)
  covalent geometry    : bond        0.00411 ( 4610)
  covalent geometry    : angle       0.60480 ( 6330)
  Misc. bond           : bond        0.07540 (    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
  77 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7886 (tptp) cc_final: 0.7513 (mptt)
REVERT: B   21 ASP cc_start: 0.6279 (OUTLIER) cc_final: 0.5901 (m-30)
REVERT: B   26 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7409 (mm-30)
REVERT: D   17 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8039 (mtpt)
REVERT: D   66 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7987 (mtmm)
REVERT: D   82 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7369 (tppt)
REVERT: D   90 GLU cc_start: 0.7910 (tt0) cc_final: 0.7293 (tm-30)
  outliers start: 17
  outliers final: 9
  residues processed: 70
  average time/residue: 1.4546
  time to fit residues: 105.1461
Evaluate side-chains
  74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   79 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0470
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0470
   chunk 1 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.148135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.128328 restraints weight = 4505.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 1.63
r_work: 0.3438 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   4614  Z= 0.116
  Angle     :  0.559   6.082   6330  Z= 0.258
  Chirality :  0.038   0.122    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.540  80.775    620
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.74 %
    Favored  : 80.40 %
  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:  3.30 (0.36), residues: 558
  helix:  2.57 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.67 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C  58 
 PHE   0.007   0.001   PHE B 118 
 TYR   0.006   0.001   TYR B  35 
 ARG   0.007   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03197 (  341)
  hydrogen bonds       : angle       3.75878 (  978)
  covalent geometry    : bond        0.00315 ( 4610)
  covalent geometry    : angle       0.55913 ( 6330)
  Misc. bond           : bond        0.05868 (    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
  72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7861 (tptp) cc_final: 0.7464 (mptm)
REVERT: B   21 ASP cc_start: 0.6028 (OUTLIER) cc_final: 0.5787 (m-30)
REVERT: B   26 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7409 (mm-30)
REVERT: D   17 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.8002 (mtpt)
REVERT: D   66 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7945 (mtmm)
REVERT: D   82 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7354 (tppt)
REVERT: D   90 GLU cc_start: 0.7889 (tt0) cc_final: 0.7281 (tm-30)
REVERT: D  134 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7304 (m)
  outliers start: 13
  outliers final: 5
  residues processed: 66
  average time/residue: 1.4458
  time to fit residues: 98.5650
Evaluate side-chains
  68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
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   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 7 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.144778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.125129 restraints weight = 4510.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.61
r_work: 0.3411 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.097   4614  Z= 0.169
  Angle     :  0.617   7.596   6330  Z= 0.287
  Chirality :  0.042   0.132    692
  Planarity :  0.006   0.046    790
  Dihedral  :  9.778  83.876    620
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.96 %
    Favored  : 80.40 %
  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:  2.93 (0.35), residues: 558
  helix:  2.31 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.56 (0.60), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  14 
 HIS   0.005   0.001   HIS B  63 
 PHE   0.012   0.002   PHE B 118 
 TYR   0.007   0.002   TYR C 140 
 ARG   0.007   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04169 (  341)
  hydrogen bonds       : angle       3.95024 (  978)
  covalent geometry    : bond        0.00454 ( 4610)
  covalent geometry    : angle       0.61677 ( 6330)
  Misc. bond           : bond        0.08134 (    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
  73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7887 (tptp) cc_final: 0.7530 (mptt)
REVERT: C   56 LYS cc_start: 0.7956 (tttt) cc_final: 0.7435 (mptt)
REVERT: D   17 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8058 (mtpt)
REVERT: D   66 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8021 (mtmm)
REVERT: D   82 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7364 (tppt)
REVERT: D   90 GLU cc_start: 0.7933 (tt0) cc_final: 0.7288 (tm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 67
  average time/residue: 1.4826
  time to fit residues: 102.4366
Evaluate side-chains
  71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain C residue   38 THR
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain D residue   17 LYS
Chi-restraints excluded: chain D residue   66 LYS
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  134 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 117 HIS
C   9 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.146951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.127698 restraints weight = 4557.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.59
r_work: 0.3421 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   4614  Z= 0.142
  Angle     :  0.594   6.755   6330  Z= 0.276
  Chirality :  0.040   0.127    692
  Planarity :  0.006   0.046    790
  Dihedral  :  9.702  82.379    620
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.18 %
    Favored  : 80.18 %
  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:  3.02 (0.36), residues: 558
  helix:  2.39 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop :  0.50 (0.60), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  58 
 PHE   0.009   0.001   PHE B 118 
 TYR   0.006   0.001   TYR B  35 
 ARG   0.009   0.001   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  341)
  hydrogen bonds       : angle       3.88273 (  978)
  covalent geometry    : bond        0.00383 ( 4610)
  covalent geometry    : angle       0.59371 ( 6330)
  Misc. bond           : bond        0.07107 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3908.19 seconds
wall clock time: 69 minutes 27.26 seconds (4167.26 seconds total)