Starting phenix.real_space_refine
on Wed Sep 17 05:04:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqn_45816/09_2025/9cqn_45816.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqn_45816/09_2025/9cqn_45816.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqn_45816/09_2025/9cqn_45816.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqn_45816/09_2025/9cqn_45816.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqn_45816/09_2025/9cqn_45816.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqn_45816/09_2025/9cqn_45816.map"
  }
  resolution = 2.37
  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=   0.029
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    2914      2.51       5
     N     764      2.21       5
     O    1096      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 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: 4790
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1050
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
    Chain: "B"
      Number of atoms: 1110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1110
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 137}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 1050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1050
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 1110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1110
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 137}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 79
          Classifications: {'water': 79}
          Link IDs: {None: 78}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 62
          Classifications: {'water': 62}
          Link IDs: {None: 61}
    Chain: "C"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 86
          Classifications: {'water': 86}
          Link IDs: {None: 85}
    Chain: "D"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 63
          Classifications: {'water': 63}
          Link IDs: {None: 62}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O   HOH B 334 " occ=0.66
  Time building chain proxies: 1.61, per 1000 atoms: 0.34
  Number of scatterers: 4790
  At special positions: 0
  Unit cell: (77.175, 72.03, 65.415, 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    1096      8.00
     N     764      7.00
     C    2914      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 195.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 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:
      40 helices and 0 sheets defined
      87.0% 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 16
    Processing helix  chain 'A' and resid 17 through 19
      No H-bonds generated for 'chain 'A' and resid 17 through 19'
    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: 4.066A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LYS A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 137
    Processing helix  chain 'B' and resid 4 through 16
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.298A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 3.620A  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: 4.040A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.652A  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 142
    Processing helix  chain 'B' and resid 143 through 146
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 17 through 19
      No H-bonds generated for 'chain 'C' and resid 17 through 19'
    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 95 through 113
      removed outlier: 3.549A  pdb=" N   LYS C  99 " --> pdb=" O   PRO C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 3.852A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 36 through 43
      removed outlier: 4.140A  pdb=" N   GLU D  43 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 56
    Processing helix  chain 'D' and resid 57 through 77
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 85 through 95
    Processing helix  chain 'D' and resid 100 through 119
      removed outlier: 3.661A  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 142
    Processing helix  chain 'D' and resid 143 through 146

    333 hydrogen bonds defined for protein.
    942 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: 0.75

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.19 -     1.37: 1555
        1.37 -     1.56: 3049
        1.56 -     1.74: 0
        1.74 -     1.93: 19
        1.93 -     2.11: 15
  Bond restraints: 4638
  Sorted by residual:
  bond pdb=" C   VAL C  93 "
       pdb=" O   VAL C  93 "
    ideal  model  delta    sigma   weight residual
    1.238  1.191  0.047 1.13e-02 7.83e+03 1.75e+01
  bond pdb=" C   PRO B  58 "
       pdb=" O   PRO B  58 "
    ideal  model  delta    sigma   weight residual
    1.237  1.197  0.040 1.16e-02 7.43e+03 1.18e+01
  bond pdb=" N   VAL C  93 "
       pdb=" CA  VAL C  93 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.19e-02 7.06e+03 1.12e+01
  bond pdb=" C3B HEM C 201 "
       pdb=" CAB HEM C 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.478  0.066 2.00e-02 2.50e+03 1.10e+01
  bond pdb=" N   VAL C  96 "
       pdb=" CA  VAL C  96 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.01e+01
  ... (remaining 4633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 5970
        1.26 -     2.52: 270
        2.52 -     3.77: 82
        3.77 -     5.03: 26
        5.03 -     6.29: 10
  Bond angle restraints: 6358
  Sorted by residual:
  angle pdb=" CA  ASP C  94 "
        pdb=" CB  ASP C  94 "
        pdb=" CG  ASP C  94 "
      ideal   model   delta    sigma   weight residual
     112.60  117.14   -4.54 1.00e+00 1.00e+00 2.06e+01
  angle pdb=" CA  LEU C  91 "
        pdb=" C   LEU C  91 "
        pdb=" O   LEU C  91 "
      ideal   model   delta    sigma   weight residual
     120.55  115.80    4.75 1.06e+00 8.90e-01 2.01e+01
  angle pdb=" C   ASP C  94 "
        pdb=" CA  ASP C  94 "
        pdb=" CB  ASP C  94 "
      ideal   model   delta    sigma   weight residual
     109.52  115.81   -6.29 1.58e+00 4.01e-01 1.59e+01
  angle pdb=" CA  LYS C 139 "
        pdb=" C   LYS C 139 "
        pdb=" O   LYS C 139 "
      ideal   model   delta    sigma   weight residual
     120.55  116.46    4.09 1.06e+00 8.90e-01 1.49e+01
  angle pdb=" C   ASP C  94 "
        pdb=" N   PRO C  95 "
        pdb=" CA  PRO C  95 "
      ideal   model   delta    sigma   weight residual
     119.05  123.24   -4.19 1.11e+00 8.12e-01 1.42e+01
  ... (remaining 6353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 2286
       17.96 -    35.91: 240
       35.91 -    53.87: 73
       53.87 -    71.83: 17
       71.83 -    89.78: 10
  Dihedral angle restraints: 2626
    sinusoidal: 998
      harmonic: 1628
  Sorted by residual:
  dihedral pdb=" C2B HEM C 201 "
           pdb=" C3B HEM C 201 "
           pdb=" CAB HEM C 201 "
           pdb=" CBB HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -69.82   69.82     2      1.00e+01 1.00e-02 4.23e+01
  dihedral pdb=" C2C HEM C 201 "
           pdb=" C3C HEM C 201 "
           pdb=" CAC HEM C 201 "
           pdb=" CBC HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -65.25   65.25     2      1.00e+01 1.00e-02 3.96e+01
  dihedral pdb=" C1A HEM C 201 "
           pdb=" C2A HEM C 201 "
           pdb=" CAA HEM C 201 "
           pdb=" CBA HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   90.22   89.78     2      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 2623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 494
       0.038 -    0.076: 150
       0.076 -    0.114: 31
       0.114 -    0.152: 9
       0.152 -    0.191: 4
  Chirality restraints: 688
  Sorted by residual:
  chirality pdb=" CB  VAL B  60 "
            pdb=" CA  VAL B  60 "
            pdb=" CG1 VAL B  60 "
            pdb=" CG2 VAL B  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.08e-01
  chirality pdb=" CB  VAL C  93 "
            pdb=" CA  VAL C  93 "
            pdb=" CG1 VAL C  93 "
            pdb=" CG2 VAL C  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  LYS B  61 "
            pdb=" N   LYS B  61 "
            pdb=" C   LYS B  61 "
            pdb=" CB  LYS B  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.37e-01
  ... (remaining 685 not shown)

  Planarity restraints: 794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  93 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.82e+00
        pdb=" C   VAL C  93 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   VAL C  93 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASP C  94 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS C  89 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.11e+00
        pdb=" C   HIS C  89 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   HIS C  89 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS C  90 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  94 "    0.028 5.00e-02 4.00e+02   4.33e-02 3.00e+00
        pdb=" N   PRO A  95 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "    0.024 5.00e-02 4.00e+02
  ... (remaining 791 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 190
        2.70 -     3.25: 4641
        3.25 -     3.80: 8872
        3.80 -     4.35: 11643
        4.35 -     4.90: 17967
  Nonbonded interactions: 43313
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS D  92 "
            pdb="FE   HEM D 201 "
     model   vdw
     2.149 3.080
  nonbonded pdb=" NE2 HIS B  92 "
            pdb="FE   HEM B 201 "
     model   vdw
     2.174 3.080
  nonbonded pdb=" NE2 HIS A  87 "
            pdb="FE   HEM A 201 "
     model   vdw
     2.198 3.080
  nonbonded pdb=" O   HOH A 313 "
            pdb=" O   HOH A 367 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   HOH C 316 "
            pdb=" O   HOH C 372 "
     model   vdw
     2.215 3.040
  ... (remaining 43308 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=0.66 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.030
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.900
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
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      :  0.009   0.315   4642  Z= 0.283
  Angle     :  0.705   6.291   6358  Z= 0.405
  Chirality :  0.040   0.191    688
  Planarity :  0.005   0.043    794
  Dihedral  : 17.703  89.782   1574
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.74 %
    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 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:  3.59 (0.37), residues: 560
  helix:  2.59 (0.25), residues: 428
  sheet:  None (None), residues: 0
  loop :  1.85 (0.66), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  31 
 TYR   0.010   0.002   TYR C 140 
 PHE   0.008   0.001   PHE A  36 
 TRP   0.008   0.001   TRP B  37 
 HIS   0.007   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 4638)
  covalent geometry    : angle       0.70496 ( 6358)
  hydrogen bonds       : bond        0.10609 (  333)
  hydrogen bonds       : angle       4.56826 (  942)
  Misc. bond           : bond        0.24718 (    4)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7777 (mmmm) cc_final: 0.7114 (tmtt)
REVERT: A   56 LYS cc_start: 0.8257 (mttt) cc_final: 0.7788 (mmpt)
REVERT: C   11 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7476 (mttp)
REVERT: C   56 LYS cc_start: 0.8247 (mttt) cc_final: 0.7847 (mmtt)
  outliers start: 6
  outliers final: 1
  residues processed: 99
  average time/residue: 0.7994
  time to fit residues: 81.3284
Evaluate side-chains
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   84 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 127 GLN
C  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.153067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.123209 restraints weight = 4097.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.41
r_work: 0.3191 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.0950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.191   4642  Z= 0.138
  Angle     :  0.724  16.780   6358  Z= 0.275
  Chirality :  0.040   0.129    688
  Planarity :  0.005   0.046    794
  Dihedral  : 10.549  88.236    621
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.86 %
    Favored  : 82.38 %
  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:  3.62 (0.37), residues: 560
  helix:  2.51 (0.25), residues: 428
  sheet:  None (None), residues: 0
  loop :  2.27 (0.65), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  92 
 TYR   0.010   0.001   TYR D 130 
 PHE   0.010   0.002   PHE A  36 
 TRP   0.004   0.001   TRP A  14 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4638)
  covalent geometry    : angle       0.72416 ( 6358)
  hydrogen bonds       : bond        0.04114 (  333)
  hydrogen bonds       : angle       4.15869 (  942)
  Misc. bond           : bond        0.15450 (    4)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7666 (mttm) cc_final: 0.7245 (mttp)
REVERT: A   56 LYS cc_start: 0.7779 (mttt) cc_final: 0.6866 (mmpt)
REVERT: A   92 ARG cc_start: 0.8357 (mtp85) cc_final: 0.8045 (mtt-85)
REVERT: C   11 LYS cc_start: 0.7564 (mtpp) cc_final: 0.6862 (mttp)
REVERT: C   56 LYS cc_start: 0.7770 (mttt) cc_final: 0.6961 (mmtt)
REVERT: D   43 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7039 (mt-10)
REVERT: D   61 LYS cc_start: 0.8010 (mttt) cc_final: 0.7660 (mttm)
  outliers start: 8
  outliers final: 2
  residues processed: 85
  average time/residue: 0.7653
  time to fit residues: 66.9720
Evaluate side-chains
  86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.153231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.123228 restraints weight = 4025.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.40
r_work: 0.3189 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4642  Z= 0.131
  Angle     :  0.709  16.223   6358  Z= 0.266
  Chirality :  0.039   0.128    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.592  89.626    620
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.42 %
    Favored  : 82.38 %
  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:  3.72 (0.36), residues: 560
  helix:  2.56 (0.25), residues: 428
  sheet:  None (None), residues: 0
  loop :  2.37 (0.64), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  92 
 TYR   0.010   0.001   TYR B 130 
 PHE   0.009   0.001   PHE D 118 
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4638)
  covalent geometry    : angle       0.70882 ( 6358)
  hydrogen bonds       : bond        0.03896 (  333)
  hydrogen bonds       : angle       4.07402 (  942)
  Misc. bond           : bond        0.02065 (    4)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7796 (mttt) cc_final: 0.6928 (mmtt)
REVERT: A   90 LYS cc_start: 0.8358 (mppt) cc_final: 0.8082 (mppt)
REVERT: B   95 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.6831 (tmtt)
REVERT: C   11 LYS cc_start: 0.7518 (mtpp) cc_final: 0.6772 (mttt)
REVERT: C   56 LYS cc_start: 0.7767 (mttt) cc_final: 0.6939 (mmtt)
REVERT: D   43 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7060 (mt-10)
REVERT: D   61 LYS cc_start: 0.8004 (mttt) cc_final: 0.7655 (mttm)
  outliers start: 10
  outliers final: 3
  residues processed: 86
  average time/residue: 0.7587
  time to fit residues: 67.1395
Evaluate side-chains
  85 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   95 LYS
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.153579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.123520 restraints weight = 4016.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.40
r_work: 0.3192 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4642  Z= 0.126
  Angle     :  0.699  16.111   6358  Z= 0.260
  Chirality :  0.039   0.127    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.510  89.371    620
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.08 %
    Favored  : 81.50 %
  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:  3.77 (0.36), residues: 560
  helix:  2.65 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.19 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  92 
 TYR   0.010   0.001   TYR B 130 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.006   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4638)
  covalent geometry    : angle       0.69943 ( 6358)
  hydrogen bonds       : bond        0.03731 (  333)
  hydrogen bonds       : angle       4.02885 (  942)
  Misc. bond           : bond        0.02660 (    4)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7583 (mttm) cc_final: 0.7145 (mttp)
REVERT: A   56 LYS cc_start: 0.7811 (mttt) cc_final: 0.6916 (mmpt)
REVERT: A   90 LYS cc_start: 0.8365 (mppt) cc_final: 0.8110 (mppt)
REVERT: B   95 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.6769 (tmtt)
REVERT: C   11 LYS cc_start: 0.7577 (mtpp) cc_final: 0.6843 (mttt)
REVERT: C   56 LYS cc_start: 0.7773 (mttt) cc_final: 0.6957 (mmtt)
REVERT: D   43 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7032 (mt-10)
REVERT: D   61 LYS cc_start: 0.7999 (mttt) cc_final: 0.7656 (mttm)
  outliers start: 11
  outliers final: 3
  residues processed: 86
  average time/residue: 0.7058
  time to fit residues: 62.4654
Evaluate side-chains
  85 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   95 LYS
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 34 optimal weight:    0.2980
   chunk 36 optimal weight:    0.7980
   chunk 52 optimal weight:    0.3980
   chunk 32 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 24 optimal weight:    0.2980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  89 HIS
B  63 HIS
C  89 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.154321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.124333 restraints weight = 4022.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.40
r_work: 0.3206 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.1246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4642  Z= 0.116
  Angle     :  0.690  16.094   6358  Z= 0.252
  Chirality :  0.038   0.123    688
  Planarity :  0.005   0.044    794
  Dihedral  : 10.332  89.197    620
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.42 %
    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 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:  3.89 (0.36), residues: 560
  helix:  2.76 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.15 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  92 
 TYR   0.009   0.001   TYR B 130 
 PHE   0.008   0.001   PHE D 118 
 TRP   0.006   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4638)
  covalent geometry    : angle       0.68999 ( 6358)
  hydrogen bonds       : bond        0.03468 (  333)
  hydrogen bonds       : angle       3.94869 (  942)
  Misc. bond           : bond        0.01355 (    4)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7582 (mttm) cc_final: 0.7126 (mttp)
REVERT: A   56 LYS cc_start: 0.7764 (mttt) cc_final: 0.6868 (mmpt)
REVERT: A   90 LYS cc_start: 0.8350 (mppt) cc_final: 0.8088 (mppt)
REVERT: B   93 CYS cc_start: 0.6707 (m) cc_final: 0.5856 (t)
REVERT: C   11 LYS cc_start: 0.7531 (mtpp) cc_final: 0.6815 (mttp)
REVERT: C   56 LYS cc_start: 0.7739 (mttt) cc_final: 0.6913 (mmpt)
REVERT: D   43 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7006 (mt-10)
REVERT: D   61 LYS cc_start: 0.7973 (mttt) cc_final: 0.7633 (mttm)
  outliers start: 12
  outliers final: 4
  residues processed: 89
  average time/residue: 0.7297
  time to fit residues: 66.8286
Evaluate side-chains
  86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    0.4980
   chunk 1 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   chunk 51 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.153738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.123419 restraints weight = 4087.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.41
r_work: 0.3193 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4642  Z= 0.123
  Angle     :  0.696  16.183   6358  Z= 0.257
  Chirality :  0.039   0.126    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.453  89.817    620
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.08 %
    Favored  : 81.50 %
  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:  3.83 (0.36), residues: 560
  helix:  2.71 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.16 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  92 
 TYR   0.009   0.001   TYR D 130 
 PHE   0.010   0.001   PHE B 118 
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4638)
  covalent geometry    : angle       0.69620 ( 6358)
  hydrogen bonds       : bond        0.03669 (  333)
  hydrogen bonds       : angle       3.97364 (  942)
  Misc. bond           : bond        0.01873 (    4)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7600 (mttm) cc_final: 0.7112 (mttp)
REVERT: A   56 LYS cc_start: 0.7776 (mttt) cc_final: 0.6885 (mmpt)
REVERT: B   93 CYS cc_start: 0.6688 (m) cc_final: 0.5927 (t)
REVERT: C   11 LYS cc_start: 0.7567 (mtpp) cc_final: 0.6856 (mttp)
REVERT: C   56 LYS cc_start: 0.7766 (mttt) cc_final: 0.6928 (mmpt)
REVERT: D   61 LYS cc_start: 0.7988 (mttt) cc_final: 0.7651 (mttm)
  outliers start: 11
  outliers final: 4
  residues processed: 88
  average time/residue: 0.7639
  time to fit residues: 69.2348
Evaluate side-chains
  85 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain D residue   11 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.153702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.123708 restraints weight = 4010.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.39
r_work: 0.3198 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4642  Z= 0.127
  Angle     :  0.693  15.957   6358  Z= 0.261
  Chirality :  0.039   0.127    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.467  89.084    620
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.18 %
    Favored  : 81.28 %
  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:  3.79 (0.36), residues: 560
  helix:  2.69 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.11 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  92 
 TYR   0.010   0.001   TYR B 130 
 PHE   0.009   0.001   PHE C  98 
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4638)
  covalent geometry    : angle       0.69296 ( 6358)
  hydrogen bonds       : bond        0.03756 (  333)
  hydrogen bonds       : angle       3.98223 (  942)
  Misc. bond           : bond        0.02990 (    4)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7570 (mttm) cc_final: 0.7081 (mttp)
REVERT: A   56 LYS cc_start: 0.7774 (mttt) cc_final: 0.6890 (mmpt)
REVERT: B   93 CYS cc_start: 0.6683 (m) cc_final: 0.5940 (t)
REVERT: C   11 LYS cc_start: 0.7535 (mtpp) cc_final: 0.6787 (mttt)
REVERT: C   56 LYS cc_start: 0.7785 (mttt) cc_final: 0.6925 (mmpt)
REVERT: D   61 LYS cc_start: 0.7995 (mttt) cc_final: 0.7654 (mttm)
  outliers start: 7
  outliers final: 4
  residues processed: 86
  average time/residue: 0.7280
  time to fit residues: 64.5051
Evaluate side-chains
  85 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain D residue   11 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0980
   chunk 52 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.5180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.154376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.124372 restraints weight = 4054.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.41
r_work: 0.3208 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4642  Z= 0.115
  Angle     :  0.683  15.855   6358  Z= 0.251
  Chirality :  0.038   0.122    688
  Planarity :  0.005   0.044    794
  Dihedral  : 10.241  89.498    620
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.84 %
    Favored  : 80.62 %
  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:  3.89 (0.36), residues: 560
  helix:  2.77 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.10 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  92 
 TYR   0.009   0.001   TYR B 130 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.005   0.001   TRP A  14 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4638)
  covalent geometry    : angle       0.68323 ( 6358)
  hydrogen bonds       : bond        0.03415 (  333)
  hydrogen bonds       : angle       3.90298 (  942)
  Misc. bond           : bond        0.01536 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7558 (mttm) cc_final: 0.7071 (mttp)
REVERT: A   56 LYS cc_start: 0.7760 (mttt) cc_final: 0.6853 (mmpt)
REVERT: B   93 CYS cc_start: 0.6658 (m) cc_final: 0.5944 (t)
REVERT: C   11 LYS cc_start: 0.7542 (mtpp) cc_final: 0.6803 (mttt)
REVERT: C   56 LYS cc_start: 0.7739 (mttt) cc_final: 0.6937 (mmtt)
REVERT: D   61 LYS cc_start: 0.7963 (mttt) cc_final: 0.7621 (mttm)
  outliers start: 7
  outliers final: 4
  residues processed: 88
  average time/residue: 0.7728
  time to fit residues: 70.0089
Evaluate side-chains
  86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain D residue   11 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 4 optimal weight:    0.3980
   chunk 44 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.153696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.123793 restraints weight = 4006.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.39
r_work: 0.3199 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4642  Z= 0.125
  Angle     :  0.694  15.981   6358  Z= 0.259
  Chirality :  0.039   0.126    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.368  88.810    620
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 18.06 %
    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 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:  3.82 (0.36), residues: 560
  helix:  2.72 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.09 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  92 
 TYR   0.010   0.001   TYR B 130 
 PHE   0.008   0.001   PHE C  98 
 TRP   0.005   0.001   TRP A  14 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4638)
  covalent geometry    : angle       0.69391 ( 6358)
  hydrogen bonds       : bond        0.03685 (  333)
  hydrogen bonds       : angle       3.94931 (  942)
  Misc. bond           : bond        0.02269 (    4)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7533 (mttm) cc_final: 0.7037 (mttp)
REVERT: A   56 LYS cc_start: 0.7768 (mttt) cc_final: 0.6854 (mmpt)
REVERT: B   93 CYS cc_start: 0.6675 (m) cc_final: 0.5947 (t)
REVERT: C   11 LYS cc_start: 0.7558 (mtpp) cc_final: 0.6818 (mttt)
REVERT: C   56 LYS cc_start: 0.7756 (mttt) cc_final: 0.6916 (mmpt)
REVERT: D   61 LYS cc_start: 0.7982 (mttt) cc_final: 0.7639 (mttm)
  outliers start: 7
  outliers final: 4
  residues processed: 84
  average time/residue: 0.7362
  time to fit residues: 63.7188
Evaluate side-chains
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain D residue   11 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 22 optimal weight:    0.4980
   chunk 30 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    0.3980
   chunk 53 optimal weight:    0.0770
   chunk 43 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A  89 HIS
D  63 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.155465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.125434 restraints weight = 3998.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.39
r_work: 0.3220 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4642  Z= 0.110
  Angle     :  0.678  15.742   6358  Z= 0.248
  Chirality :  0.037   0.121    688
  Planarity :  0.005   0.044    794
  Dihedral  : 10.073  89.388    620
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 18.94 %
    Favored  : 80.62 %
  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:  3.94 (0.36), residues: 560
  helix:  2.82 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.08 (0.60), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  92 
 TYR   0.010   0.001   TYR D 130 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.005   0.001   TRP A  14 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 4638)
  covalent geometry    : angle       0.67793 ( 6358)
  hydrogen bonds       : bond        0.03287 (  333)
  hydrogen bonds       : angle       3.85709 (  942)
  Misc. bond           : bond        0.01328 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7584 (mttm) cc_final: 0.7094 (mttp)
REVERT: A   56 LYS cc_start: 0.7765 (mttt) cc_final: 0.6880 (mmpt)
REVERT: B   93 CYS cc_start: 0.6642 (m) cc_final: 0.5934 (t)
REVERT: B  121 GLU cc_start: 0.7725 (pt0) cc_final: 0.7495 (pt0)
REVERT: C   11 LYS cc_start: 0.7543 (mtpp) cc_final: 0.6825 (mttp)
REVERT: C   56 LYS cc_start: 0.7727 (mttt) cc_final: 0.6893 (mmpt)
REVERT: D   61 LYS cc_start: 0.7960 (mttt) cc_final: 0.7625 (mttm)
  outliers start: 2
  outliers final: 2
  residues processed: 84
  average time/residue: 0.7188
  time to fit residues: 62.0817
Evaluate side-chains
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain B residue   11 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 1 optimal weight:    0.4980
   chunk 34 optimal weight:    0.3980
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.5980

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.154423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.124299 restraints weight = 4002.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.39
r_work: 0.3204 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4642  Z= 0.121
  Angle     :  0.689  15.992   6358  Z= 0.256
  Chirality :  0.039   0.125    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.231  88.174    620
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 18.94 %
    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 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:  3.87 (0.36), residues: 560
  helix:  2.76 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.09 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  92 
 TYR   0.010   0.001   TYR D 130 
 PHE   0.010   0.001   PHE B 118 
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4638)
  covalent geometry    : angle       0.68908 ( 6358)
  hydrogen bonds       : bond        0.03600 (  333)
  hydrogen bonds       : angle       3.91007 (  942)
  Misc. bond           : bond        0.01969 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2312.87 seconds
wall clock time: 40 minutes 5.97 seconds (2405.97 seconds total)