Starting phenix.real_space_refine
on Fri Aug 22 15:12:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqm_45815/08_2025/9cqm_45815.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqm_45815/08_2025/9cqm_45815.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqm_45815/08_2025/9cqm_45815.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqm_45815/08_2025/9cqm_45815.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqm_45815/08_2025/9cqm_45815.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqm_45815/08_2025/9cqm_45815.map"
  }
  resolution = 2.55
  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=   0.025
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 1.06, per 1000 atoms: 0.22
  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: 0.38
  Conformation dependent library (CDL) restraints added in 127.2 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: 0.14
  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: 0.89

  Time building geometry restraints manager: 0.46 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:             3.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.360
  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:9.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
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
  99 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8184 (mttt) cc_final: 0.7720 (mmpt)
REVERT: A   90 LYS cc_start: 0.8306 (mppt) cc_final: 0.7907 (ttmt)
REVERT: C   11 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7980 (mttp)
REVERT: D   26 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7955 (mm-30)
REVERT: D   52 ASP cc_start: 0.8058 (m-30) cc_final: 0.7852 (m-30)
  outliers start: 6
  outliers final: 0
  residues processed: 96
  average time/residue: 0.7147
  time to fit residues: 70.4436
Evaluate side-chains
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0570
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
B 139 ASN
C  89 HIS
D  19 ASN
D  63 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.146241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.122234 restraints weight = 4483.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.22
r_work: 0.3161 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3013
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    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 = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3013
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.198   4642  Z= 0.123
  Angle     :  0.701  16.345   6358  Z= 0.264
  Chirality :  0.038   0.131    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.751  86.456    620
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.08 %
    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:  3.80 (0.37), residues: 560
  helix:  2.63 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.35 (0.64), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  92 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.005   0.001   TRP C  14 
 HIS   0.005   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4638)
  covalent geometry    : angle       0.70053 ( 6358)
  hydrogen bonds       : bond        0.03604 (  333)
  hydrogen bonds       : angle       3.94804 (  942)
  Misc. bond           : bond        0.12158 (    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
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7628 (tttt)
REVERT: A   92 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8029 (mtp85)
REVERT: B   26 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7179 (tm-30)
REVERT: B   43 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7053 (mp0)
REVERT: C   85 ASP cc_start: 0.7900 (m-30) cc_final: 0.7466 (t0)
REVERT: D   26 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7563 (mm-30)
REVERT: D  101 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7202 (tm-30)
REVERT: D  132 LYS cc_start: 0.8254 (mttt) cc_final: 0.8037 (mttt)
  outliers start: 9
  outliers final: 3
  residues processed: 76
  average time/residue: 0.6547
  time to fit residues: 51.3635
Evaluate side-chains
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    0.2980
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   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**
B  63 HIS
B 139 ASN
D  19 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.144963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.120886 restraints weight = 4414.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 1.21
r_work: 0.3126 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2969
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2969
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.278   4642  Z= 0.127
  Angle     :  0.729  17.100   6358  Z= 0.263
  Chirality :  0.039   0.138    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.880  87.039    620
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.74 %
    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:  2.64 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.43 (0.64), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.009   0.001   TYR B  35 
 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        0.00298 ( 4638)
  covalent geometry    : angle       0.72906 ( 6358)
  hydrogen bonds       : bond        0.03655 (  333)
  hydrogen bonds       : angle       3.94863 (  942)
  Misc. bond           : bond        0.13928 (    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
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7734 (tttt)
REVERT: A   92 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8054 (mtp85)
REVERT: B   26 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7273 (tm-30)
REVERT: C   56 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7293 (mttm)
REVERT: C   76 MET cc_start: 0.7244 (mtp) cc_final: 0.6991 (mtp)
REVERT: D   26 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7622 (mm-30)
REVERT: D   52 ASP cc_start: 0.7791 (m-30) cc_final: 0.7260 (m-30)
REVERT: D  101 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.6622 (tm-30)
REVERT: D  104 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7233 (mtt-85)
REVERT: D  132 LYS cc_start: 0.8367 (mttt) cc_final: 0.8146 (mttt)
  outliers start: 8
  outliers final: 2
  residues processed: 73
  average time/residue: 0.6441
  time to fit residues: 48.5261
Evaluate side-chains
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  104 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 39 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.141672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.117588 restraints weight = 4461.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 1.21
r_work: 0.3103 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.394   4642  Z= 0.148
  Angle     :  0.736  16.961   6358  Z= 0.273
  Chirality :  0.040   0.147    688
  Planarity :  0.005   0.046    794
  Dihedral  : 10.044  89.811    620
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.86 %
    Favored  : 81.72 %
  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:  3.67 (0.36), residues: 560
  helix:  2.53 (0.24), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.37 (0.65), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.010   0.001   TYR B  35 
 PHE   0.011   0.002   PHE B 118 
 TRP   0.007   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4638)
  covalent geometry    : angle       0.73566 ( 6358)
  hydrogen bonds       : bond        0.03989 (  333)
  hydrogen bonds       : angle       4.05341 (  942)
  Misc. bond           : bond        0.20217 (    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
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7833 (mttt) cc_final: 0.6977 (mptt)
REVERT: A   90 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7787 (tttt)
REVERT: A  116 GLU cc_start: 0.7722 (mp0) cc_final: 0.7054 (pp20)
REVERT: B   26 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7289 (tm-30)
REVERT: B   43 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7066 (mp0)
REVERT: C   76 MET cc_start: 0.7217 (mtp) cc_final: 0.6959 (mtp)
REVERT: C   90 LYS cc_start: 0.8083 (mttt) cc_final: 0.7538 (ttpt)
REVERT: D   26 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7602 (mm-30)
REVERT: D  101 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6760 (tm-30)
REVERT: D  132 LYS cc_start: 0.8410 (mttt) cc_final: 0.8152 (mttt)
  outliers start: 11
  outliers final: 4
  residues processed: 77
  average time/residue: 0.6887
  time to fit residues: 54.6897
Evaluate side-chains
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0050
   chunk 34 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 52 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.5594

-------------------------------------------------------------------------------
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  20 HIS
C  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.145098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.121526 restraints weight = 4439.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.20
r_work: 0.3127 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.290   4642  Z= 0.119
  Angle     :  0.712  17.100   6358  Z= 0.255
  Chirality :  0.038   0.137    688
  Planarity :  0.005   0.046    794
  Dihedral  :  9.666  88.926    620
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  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:  3.89 (0.36), residues: 560
  helix:  2.71 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.34 (0.63), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B 130 
 PHE   0.007   0.001   PHE B 118 
 TRP   0.007   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4638)
  covalent geometry    : angle       0.71228 ( 6358)
  hydrogen bonds       : bond        0.03353 (  333)
  hydrogen bonds       : angle       3.89959 (  942)
  Misc. bond           : bond        0.14895 (    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
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7756 (tttt)
REVERT: A  116 GLU cc_start: 0.7630 (mp0) cc_final: 0.7128 (pp20)
REVERT: B   26 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7285 (tm-30)
REVERT: B   43 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7053 (mp0)
REVERT: C   11 LYS cc_start: 0.7701 (mtpp) cc_final: 0.7254 (mttp)
REVERT: C   56 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7254 (mttm)
REVERT: C   60 LYS cc_start: 0.8185 (tptp) cc_final: 0.7971 (tptm)
REVERT: C   76 MET cc_start: 0.7217 (mtp) cc_final: 0.6957 (mtp)
REVERT: C   90 LYS cc_start: 0.8085 (mttt) cc_final: 0.7506 (ttpt)
REVERT: D   26 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7613 (mm-30)
REVERT: D  101 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.6616 (tm-30)
REVERT: D  104 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7288 (mtt-85)
REVERT: D  132 LYS cc_start: 0.8393 (mttt) cc_final: 0.8170 (mttt)
  outliers start: 11
  outliers final: 4
  residues processed: 77
  average time/residue: 0.6243
  time to fit residues: 49.6318
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  104 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0670
   chunk 51 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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  20 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.143146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.119161 restraints weight = 4535.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.22
r_work: 0.3110 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2950
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2950
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.315   4642  Z= 0.125
  Angle     :  0.711  16.789   6358  Z= 0.256
  Chirality :  0.039   0.137    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.700  85.937    620
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.42 %
    Favored  : 81.72 %
  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:  3.84 (0.36), residues: 560
  helix:  2.69 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.27 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B 130 
 PHE   0.008   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4638)
  covalent geometry    : angle       0.71080 ( 6358)
  hydrogen bonds       : bond        0.03523 (  333)
  hydrogen bonds       : angle       3.91679 (  942)
  Misc. bond           : bond        0.16260 (    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
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7754 (ttmt)
REVERT: A  116 GLU cc_start: 0.7581 (mp0) cc_final: 0.7189 (pp20)
REVERT: B   26 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7290 (tm-30)
REVERT: B   43 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7073 (mp0)
REVERT: C   56 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7160 (mptt)
REVERT: C   76 MET cc_start: 0.7189 (mtp) cc_final: 0.6926 (mtp)
REVERT: C   85 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7469 (t0)
REVERT: C   90 LYS cc_start: 0.8042 (mttt) cc_final: 0.7512 (ttpt)
REVERT: D   26 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7618 (mm-30)
REVERT: D  101 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6779 (tm-30)
REVERT: D  132 LYS cc_start: 0.8412 (mttt) cc_final: 0.8166 (mttt)
  outliers start: 13
  outliers final: 6
  residues processed: 73
  average time/residue: 0.5841
  time to fit residues: 43.9870
Evaluate side-chains
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0050
   chunk 41 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.6394

-------------------------------------------------------------------------------
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 139 ASN
C  20 HIS
C  72 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.143208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.119337 restraints weight = 4456.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.21
r_work: 0.3109 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.312   4642  Z= 0.124
  Angle     :  0.707  16.812   6358  Z= 0.255
  Chirality :  0.039   0.138    688
  Planarity :  0.005   0.046    794
  Dihedral  :  9.625  86.294    620
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.20 %
    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:  3.86 (0.36), residues: 560
  helix:  2.70 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.26 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B 130 
 PHE   0.008   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4638)
  covalent geometry    : angle       0.70687 ( 6358)
  hydrogen bonds       : bond        0.03456 (  333)
  hydrogen bonds       : angle       3.90172 (  942)
  Misc. bond           : bond        0.16133 (    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
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7766 (ttmt)
REVERT: A   92 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8057 (mtp85)
REVERT: A  116 GLU cc_start: 0.7588 (mp0) cc_final: 0.7243 (pp20)
REVERT: B   26 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7242 (tm-30)
REVERT: B   43 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7045 (mp0)
REVERT: C    7 LYS cc_start: 0.6541 (mttm) cc_final: 0.6271 (mttt)
REVERT: C   56 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7184 (mptt)
REVERT: C   76 MET cc_start: 0.7216 (mtp) cc_final: 0.6950 (mtp)
REVERT: C   85 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7480 (t0)
REVERT: C   90 LYS cc_start: 0.8042 (mttt) cc_final: 0.7532 (ttpt)
REVERT: D   26 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7628 (mm-30)
REVERT: D  101 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.6622 (tm-30)
REVERT: D  104 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7316 (mtt-85)
REVERT: D  132 LYS cc_start: 0.8420 (mttt) cc_final: 0.8176 (mttt)
  outliers start: 16
  outliers final: 6
  residues processed: 77
  average time/residue: 0.6424
  time to fit residues: 51.1101
Evaluate side-chains
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  104 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    0.4980
   chunk 21 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 30 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   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**
C  20 HIS
C  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.143120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.119186 restraints weight = 4526.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.22
r_work: 0.3115 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.295   4642  Z= 0.120
  Angle     :  0.703  16.741   6358  Z= 0.253
  Chirality :  0.038   0.135    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.581  86.284    620
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.08 %
    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 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:  3.92 (0.36), residues: 560
  helix:  2.74 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.31 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B 130 
 PHE   0.008   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4638)
  covalent geometry    : angle       0.70294 ( 6358)
  hydrogen bonds       : bond        0.03374 (  333)
  hydrogen bonds       : angle       3.87693 (  942)
  Misc. bond           : bond        0.15195 (    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
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7746 (tttt)
REVERT: A  116 GLU cc_start: 0.7557 (mp0) cc_final: 0.7214 (pp20)
REVERT: B   26 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7245 (tm-30)
REVERT: B   43 GLU cc_start: 0.7651 (mt-10) cc_final: 0.6992 (mp0)
REVERT: C   56 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7132 (mptt)
REVERT: C   76 MET cc_start: 0.7194 (mtp) cc_final: 0.6930 (mtp)
REVERT: C   85 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7451 (t0)
REVERT: C   90 LYS cc_start: 0.8035 (mttt) cc_final: 0.7507 (ttpt)
REVERT: D   26 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7595 (mm-30)
REVERT: D   82 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7490 (mptt)
REVERT: D  101 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6742 (tm-30)
REVERT: D  132 LYS cc_start: 0.8408 (mttt) cc_final: 0.8159 (mttt)
  outliers start: 13
  outliers final: 6
  residues processed: 74
  average time/residue: 0.6589
  time to fit residues: 50.3217
Evaluate side-chains
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0170
   chunk 12 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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  20 HIS
C  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.143766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.120030 restraints weight = 4465.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.20
r_work: 0.3122 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2972
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2972
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.271   4642  Z= 0.115
  Angle     :  0.694  16.522   6358  Z= 0.250
  Chirality :  0.038   0.132    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.512  86.120    620
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.42 %
    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:  3.97 (0.36), residues: 560
  helix:  2.78 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.31 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B 130 
 PHE   0.007   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4638)
  covalent geometry    : angle       0.69373 ( 6358)
  hydrogen bonds       : bond        0.03267 (  333)
  hydrogen bonds       : angle       3.83348 (  942)
  Misc. bond           : bond        0.13951 (    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
  81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7734 (tttt)
REVERT: A   92 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8002 (mtp85)
REVERT: A  116 GLU cc_start: 0.7508 (mp0) cc_final: 0.7171 (pp20)
REVERT: B   26 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7234 (tm-30)
REVERT: C   56 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7115 (mptt)
REVERT: C   76 MET cc_start: 0.7202 (mtp) cc_final: 0.6934 (mtp)
REVERT: C   85 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7447 (t0)
REVERT: C   90 LYS cc_start: 0.8041 (mttt) cc_final: 0.7509 (ttpt)
REVERT: D   26 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7576 (mm-30)
REVERT: D  101 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6594 (tm-30)
REVERT: D  104 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7293 (mtt-85)
REVERT: D  132 LYS cc_start: 0.8388 (mttt) cc_final: 0.8144 (mttt)
  outliers start: 14
  outliers final: 7
  residues processed: 74
  average time/residue: 0.6700
  time to fit residues: 51.2655
Evaluate side-chains
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  104 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 2 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 ** both conformations clash, **PLEASE CHECK MANUALLY**
C  20 HIS
C  68 ASN
C  72 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.142725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.118943 restraints weight = 4476.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 1.21
r_work: 0.3103 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.334   4642  Z= 0.131
  Angle     :  0.716  16.715   6358  Z= 0.262
  Chirality :  0.039   0.139    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.686  86.351    620
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  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 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:  2.67 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.27 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4638)
  covalent geometry    : angle       0.71613 ( 6358)
  hydrogen bonds       : bond        0.03620 (  333)
  hydrogen bonds       : angle       3.92248 (  942)
  Misc. bond           : bond        0.17311 (    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
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7873 (mttt) cc_final: 0.7024 (mptt)
REVERT: A   90 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7782 (tttt)
REVERT: A  116 GLU cc_start: 0.7546 (mp0) cc_final: 0.7202 (pp20)
REVERT: B   26 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7257 (tm-30)
REVERT: C   56 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7169 (mptt)
REVERT: C   60 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7992 (tptp)
REVERT: C   76 MET cc_start: 0.7190 (mtp) cc_final: 0.6927 (mtp)
REVERT: C   90 LYS cc_start: 0.8045 (mttt) cc_final: 0.7541 (ttpt)
REVERT: D   26 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7615 (mm-30)
REVERT: D   82 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7502 (mptt)
REVERT: D  101 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6637 (tm-30)
REVERT: D  104 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7534 (mtp-110)
  outliers start: 16
  outliers final: 8
  residues processed: 76
  average time/residue: 0.7183
  time to fit residues: 56.3180
Evaluate side-chains
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain C residue   60 LYS
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  104 ARG
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:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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  20 HIS
C  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.143007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.119265 restraints weight = 4457.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.21
r_work: 0.3103 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2953
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.363   4642  Z= 0.135
  Angle     :  0.719  16.788   6358  Z= 0.263
  Chirality :  0.039   0.142    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.687  86.441    620
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 14.98 %
    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:  3.78 (0.36), residues: 560
  helix:  2.65 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.23 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.009   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4638)
  covalent geometry    : angle       0.71870 ( 6358)
  hydrogen bonds       : bond        0.03667 (  333)
  hydrogen bonds       : angle       3.93990 (  942)
  Misc. bond           : bond        0.18827 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1867.47 seconds
wall clock time: 32 minutes 35.67 seconds (1955.67 seconds total)