Starting phenix.real_space_refine
on Thu Jun  5 01:21:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqm_45815/06_2025/9cqm_45815.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqm_45815/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqm_45815/06_2025/9cqm_45815.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqm_45815/06_2025/9cqm_45815.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqm_45815/06_2025/9cqm_45815.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqm_45815/06_2025/9cqm_45815.cif"
  }
  resolution = 2.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.025
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.45, per 1000 atoms: 0.93
  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: 1.24
  Conformation dependent library (CDL) restraints added in 520.8 milliseconds
  

  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: 0.43
  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: 1.40

  Time building geometry restraints manager: 1.44 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             21.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.720
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:16.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.700
-------------------------------------------------------------------------------
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 : 5.83
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.59 (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
 TRP   0.008   0.001   TRP B  37 
 HIS   0.007   0.001   HIS B  63 
 PHE   0.008   0.001   PHE A  36 
 TYR   0.010   0.002   TYR C 140 
 ARG   0.003   0.001   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10609 (  333)
  hydrogen bonds       : angle       4.56826 (  942)
  covalent geometry    : bond        0.00591 ( 4638)
  covalent geometry    : angle       0.70496 ( 6358)
  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  : 0.476 
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: 1.5784
  time to fit residues: 156.1650
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  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 21 optimal weight:    0.2980
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 ASN
C  89 HIS
D  19 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.146422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.123002 restraints weight = 4383.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.18
r_work: 0.3155 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    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 = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.222   4642  Z= 0.132
  Angle     :  0.735  17.491   6358  Z= 0.271
  Chirality :  0.039   0.135    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.862  86.634    620
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.72 (0.37), residues: 560
  helix:  2.57 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.33 (0.64), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  14 
 HIS   0.006   0.001   HIS A  87 
 PHE   0.009   0.001   PHE B 118 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.003   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03771 (  333)
  hydrogen bonds       : angle       4.00193 (  942)
  covalent geometry    : bond        0.00308 ( 4638)
  covalent geometry    : angle       0.73469 ( 6358)
  Misc. bond           : bond        0.14063 (    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
  81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7676 (tttt)
REVERT: A   92 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8044 (mtp85)
REVERT: B   26 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7229 (tm-30)
REVERT: B   43 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7033 (mp0)
REVERT: D   26 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7596 (mm-30)
REVERT: D   52 ASP cc_start: 0.7803 (m-30) cc_final: 0.7491 (m-30)
REVERT: D  101 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7266 (tm-30)
REVERT: D  132 LYS cc_start: 0.8277 (mttt) cc_final: 0.8045 (mtpt)
  outliers start: 9
  outliers final: 3
  residues processed: 77
  average time/residue: 1.4173
  time to fit residues: 112.9219
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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 28 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0770
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.144385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.120304 restraints weight = 4437.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.21
r_work: 0.3133 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2978
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2978
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.273   4642  Z= 0.121
  Angle     :  0.720  17.163   6358  Z= 0.258
  Chirality :  0.038   0.135    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.797  86.380    620
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.88 (0.36), residues: 560
  helix:  2.68 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.43 (0.64), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 
 PHE   0.008   0.001   PHE B 118 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.002   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03494 (  333)
  hydrogen bonds       : angle       3.90715 (  942)
  covalent geometry    : bond        0.00285 ( 4638)
  covalent geometry    : angle       0.72045 ( 6358)
  Misc. bond           : bond        0.13860 (    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
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.473 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7714 (tttt)
REVERT: A   92 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8034 (mtp85)
REVERT: B   26 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7277 (tm-30)
REVERT: C   56 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7257 (mttm)
REVERT: C   60 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8010 (tptt)
REVERT: C   76 MET cc_start: 0.7237 (mtp) cc_final: 0.6984 (mtp)
REVERT: C   85 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7478 (t0)
REVERT: D   26 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7583 (mm-30)
REVERT: D  101 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.6587 (tm-30)
REVERT: D  104 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7219 (mtt-85)
REVERT: D  132 LYS cc_start: 0.8344 (mttt) cc_final: 0.8131 (mttt)
  outliers start: 9
  outliers final: 2
  residues processed: 74
  average time/residue: 1.4720
  time to fit residues: 112.6364
Evaluate side-chains
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
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 C residue   60 LYS
Chi-restraints excluded: chain C residue   85 ASP
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 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 ASN
D  19 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.144333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.120338 restraints weight = 4452.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.22
r_work: 0.3114 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    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 = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.330   4642  Z= 0.135
  Angle     :  0.726  17.136   6358  Z= 0.265
  Chirality :  0.039   0.141    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.915  89.875    620
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.20 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.80 (0.36), residues: 560
  helix:  2.62 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.39 (0.65), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 
 PHE   0.009   0.001   PHE B 118 
 TYR   0.009   0.001   TYR B  35 
 ARG   0.002   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03764 (  333)
  hydrogen bonds       : angle       3.98239 (  942)
  covalent geometry    : bond        0.00317 ( 4638)
  covalent geometry    : angle       0.72601 ( 6358)
  Misc. bond           : bond        0.17379 (    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: 13
    poor density    : 69
  time to evaluate  : 0.645 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7788 (tttt)
REVERT: A   92 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8064 (mtp85)
REVERT: B   26 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7274 (tm-30)
REVERT: B   43 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7050 (mp0)
REVERT: C   60 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8029 (tptt)
REVERT: C   76 MET cc_start: 0.7213 (mtp) cc_final: 0.6950 (mtp)
REVERT: D   26 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7591 (mm-30)
REVERT: D  101 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6739 (tm-30)
REVERT: D  132 LYS cc_start: 0.8395 (mttt) cc_final: 0.8150 (mttt)
  outliers start: 13
  outliers final: 3
  residues processed: 76
  average time/residue: 1.4749
  time to fit residues: 115.9371
Evaluate side-chains
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
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 C residue   60 LYS
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0070
   chunk 1 optimal weight:    0.8980
   chunk 30 optimal weight:    0.2980
   chunk 18 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4998

-------------------------------------------------------------------------------
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  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.144611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.120397 restraints weight = 4532.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.23
r_work: 0.3133 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.254   4642  Z= 0.114
  Angle     :  0.704  16.891   6358  Z= 0.251
  Chirality :  0.038   0.132    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.610  89.175    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.00 (0.36), residues: 560
  helix:  2.79 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.37 (0.63), residues: 134

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03234 (  333)
  hydrogen bonds       : angle       3.83984 (  942)
  covalent geometry    : bond        0.00272 ( 4638)
  covalent geometry    : angle       0.70395 ( 6358)
  Misc. bond           : bond        0.13272 (    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
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7726 (tttt)
REVERT: A   92 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8002 (mtp85)
REVERT: B   26 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7242 (tm-30)
REVERT: B   43 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6929 (mp0)
REVERT: C   56 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7212 (mttm)
REVERT: C   60 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8033 (tptt)
REVERT: C   76 MET cc_start: 0.7192 (mtp) cc_final: 0.6933 (mtp)
REVERT: C   85 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7459 (t0)
REVERT: D   26 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7560 (mm-30)
REVERT: D  101 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6573 (tm-30)
REVERT: D  104 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7241 (mtt-85)
REVERT: D  132 LYS cc_start: 0.8371 (mttt) cc_final: 0.8149 (mttt)
  outliers start: 14
  outliers final: 4
  residues processed: 77
  average time/residue: 1.3659
  time to fit residues: 108.8572
Evaluate side-chains
  78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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   26 GLU
Chi-restraints excluded: chain C residue   60 LYS
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
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 1 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0980
   chunk 24 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.143261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.119218 restraints weight = 4468.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.22
r_work: 0.3110 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.306   4642  Z= 0.126
  Angle     :  0.713  16.806   6358  Z= 0.258
  Chirality :  0.039   0.137    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.686  85.972    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 :  3.30 %
    Allowed  : 15.64 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.87 (0.36), residues: 560
  helix:  2.70 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.30 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 
 PHE   0.008   0.001   PHE C  98 
 TYR   0.008   0.001   TYR B 130 
 ARG   0.002   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  333)
  hydrogen bonds       : angle       3.91268 (  942)
  covalent geometry    : bond        0.00297 ( 4638)
  covalent geometry    : angle       0.71264 ( 6358)
  Misc. bond           : bond        0.16094 (    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
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7740 (ttmt)
REVERT: A   92 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8053 (mtp85)
REVERT: A  116 GLU cc_start: 0.7517 (mp0) cc_final: 0.7065 (pp20)
REVERT: B   26 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7277 (tm-30)
REVERT: B   43 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7062 (mp0)
REVERT: B  144 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6394 (mptm)
REVERT: C   56 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7095 (mptt)
REVERT: C   60 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8016 (tptt)
REVERT: C   76 MET cc_start: 0.7199 (mtp) cc_final: 0.6942 (mtp)
REVERT: C   85 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7452 (t0)
REVERT: C   90 LYS cc_start: 0.8036 (mttt) cc_final: 0.7486 (ttpt)
REVERT: D   26 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7602 (mm-30)
REVERT: D  101 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6759 (tm-30)
REVERT: D  132 LYS cc_start: 0.8394 (mttt) cc_final: 0.8144 (mttt)
  outliers start: 15
  outliers final: 6
  residues processed: 76
  average time/residue: 1.4515
  time to fit residues: 114.1065
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  : 0.521 
-------------------------------------------------------------------------------
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 B residue  144 LYS
Chi-restraints excluded: chain C residue   60 LYS
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   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  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.142448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.118661 restraints weight = 4421.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.20
r_work: 0.3136 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    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 = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.351   4642  Z= 0.132
  Angle     :  0.721  17.005   6358  Z= 0.261
  Chirality :  0.039   0.142    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.683  86.407    620
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.42 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.80 (0.36), residues: 560
  helix:  2.66 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.27 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 
 PHE   0.009   0.001   PHE B 118 
 TYR   0.008   0.001   TYR B 130 
 ARG   0.001   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03613 (  333)
  hydrogen bonds       : angle       3.95362 (  942)
  covalent geometry    : bond        0.00312 ( 4638)
  covalent geometry    : angle       0.72060 ( 6358)
  Misc. bond           : bond        0.18436 (    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
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7836 (mttt) cc_final: 0.6978 (mptt)
REVERT: A   90 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7779 (tttt)
REVERT: A  116 GLU cc_start: 0.7451 (mp0) cc_final: 0.7102 (pp20)
REVERT: B   26 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7214 (tm-30)
REVERT: B   43 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7008 (mp0)
REVERT: C   56 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7098 (mptt)
REVERT: C   60 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8000 (tptt)
REVERT: C   76 MET cc_start: 0.7197 (mtp) cc_final: 0.6934 (mtp)
REVERT: C   90 LYS cc_start: 0.8032 (mttt) cc_final: 0.7503 (ttpt)
REVERT: D   26 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7574 (mm-30)
REVERT: D  101 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6603 (tm-30)
REVERT: D  104 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7488 (mtp-110)
  outliers start: 16
  outliers final: 8
  residues processed: 77
  average time/residue: 1.4448
  time to fit residues: 115.2819
Evaluate side-chains
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
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   85 ASP
Chi-restraints excluded: chain D residue   11 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 18 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3554 r_free = 0.3554 target = 0.143504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.120040 restraints weight = 4436.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 1.20
r_work: 0.3105 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2954
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2954 r_free = 0.2954    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2954 r_free = 0.2954    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2954
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.352   4642  Z= 0.131
  Angle     :  0.715  16.920   6358  Z= 0.260
  Chirality :  0.039   0.140    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.641  85.888    620
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.93
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.82 (0.36), residues: 560
  helix:  2.66 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.28 (0.62), residues: 134

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03613 (  333)
  hydrogen bonds       : angle       3.93418 (  942)
  covalent geometry    : bond        0.00311 ( 4638)
  covalent geometry    : angle       0.71507 ( 6358)
  Misc. bond           : bond        0.18367 (    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
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.818 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7872 (mttt) cc_final: 0.7030 (mptt)
REVERT: A   90 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7768 (ttmt)
REVERT: A  116 GLU cc_start: 0.7424 (mp0) cc_final: 0.7118 (pp20)
REVERT: B   26 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7255 (tm-30)
REVERT: B   43 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7030 (mp0)
REVERT: B  144 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6365 (mptm)
REVERT: C   56 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7154 (mptt)
REVERT: C   60 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8035 (tptt)
REVERT: C   76 MET cc_start: 0.7205 (mtp) cc_final: 0.6933 (mtp)
REVERT: C   90 LYS cc_start: 0.8040 (mttt) cc_final: 0.7531 (ttpt)
REVERT: D   26 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7605 (mm-30)
REVERT: D  101 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6791 (tm-30)
REVERT: D  132 LYS cc_start: 0.8328 (mttt) cc_final: 0.8115 (mtpt)
  outliers start: 13
  outliers final: 7
  residues processed: 76
  average time/residue: 1.5747
  time to fit residues: 124.2067
Evaluate side-chains
  81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
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 B residue  144 LYS
Chi-restraints excluded: chain C residue   60 LYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3538 r_free = 0.3538 target = 0.142425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.118511 restraints weight = 4485.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.21
r_work: 0.3099 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    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 = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.350   4642  Z= 0.132
  Angle     :  0.718  17.007   6358  Z= 0.261
  Chirality :  0.039   0.141    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.636  86.181    620
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.86 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.80 (0.36), residues: 560
  helix:  2.65 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.29 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 
 PHE   0.009   0.001   PHE B 118 
 TYR   0.009   0.001   TYR B  35 
 ARG   0.001   0.000   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03607 (  333)
  hydrogen bonds       : angle       3.93728 (  942)
  covalent geometry    : bond        0.00313 ( 4638)
  covalent geometry    : angle       0.71767 ( 6358)
  Misc. bond           : bond        0.18349 (    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
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7870 (mttt) cc_final: 0.7026 (mptt)
REVERT: A   90 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7789 (tttt)
REVERT: A  116 GLU cc_start: 0.7412 (mp0) cc_final: 0.7118 (pp20)
REVERT: B   26 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7259 (tm-30)
REVERT: B   43 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7016 (mp0)
REVERT: C   56 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7151 (mptt)
REVERT: C   60 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8031 (tptt)
REVERT: C   76 MET cc_start: 0.7204 (mtp) cc_final: 0.6926 (mtp)
REVERT: C   90 LYS cc_start: 0.8059 (mttt) cc_final: 0.7545 (ttpt)
REVERT: D   26 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7603 (mm-30)
REVERT: D  101 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.6611 (tm-30)
REVERT: D  104 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7318 (mtt-85)
REVERT: D  132 LYS cc_start: 0.8338 (mttt) cc_final: 0.8132 (mttt)
  outliers start: 15
  outliers final: 8
  residues processed: 73
  average time/residue: 1.5805
  time to fit residues: 119.5540
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  : 0.482 
-------------------------------------------------------------------------------
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3538 r_free = 0.3538 target = 0.142389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.118832 restraints weight = 4465.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.20
r_work: 0.3113 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.335   4642  Z= 0.128
  Angle     :  0.712  16.992   6358  Z= 0.258
  Chirality :  0.039   0.138    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.586  85.975    620
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.08 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.83 (0.36), residues: 560
  helix:  2.69 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.26 (0.61), residues: 134

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03524 (  333)
  hydrogen bonds       : angle       3.91425 (  942)
  covalent geometry    : bond        0.00303 ( 4638)
  covalent geometry    : angle       0.71207 ( 6358)
  Misc. bond           : bond        0.17535 (    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
  78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7753 (tttt)
REVERT: A  116 GLU cc_start: 0.7453 (mp0) cc_final: 0.7080 (pp20)
REVERT: B   26 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7238 (tm-30)
REVERT: B   43 GLU cc_start: 0.7658 (mt-10) cc_final: 0.6995 (mp0)
REVERT: C   56 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7096 (mptt)
REVERT: C   60 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8009 (tptt)
REVERT: C   76 MET cc_start: 0.7185 (mtp) cc_final: 0.6898 (mtp)
REVERT: C   85 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7489 (t0)
REVERT: C   90 LYS cc_start: 0.8054 (mttt) cc_final: 0.7533 (ttpt)
REVERT: D   26 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7565 (mm-30)
REVERT: D  101 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6570 (tm-30)
REVERT: D  104 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7288 (mtt-85)
REVERT: D  132 LYS cc_start: 0.8324 (mttt) cc_final: 0.8069 (mttt)
  outliers start: 14
  outliers final: 7
  residues processed: 71
  average time/residue: 1.5955
  time to fit residues: 117.5065
Evaluate side-chains
  78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    0.2980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C  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 = 0.3551 r_free = 0.3551 target = 0.143522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.119974 restraints weight = 4453.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.20
r_work: 0.3119 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
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   0.287   4642  Z= 0.117
  Angle     :  0.701  16.987   6358  Z= 0.251
  Chirality :  0.038   0.134    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.485  86.072    620
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.86 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.93 (0.36), residues: 560
  helix:  2.76 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.25 (0.61), residues: 134

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03312 (  333)
  hydrogen bonds       : angle       3.85390 (  942)
  covalent geometry    : bond        0.00279 ( 4638)
  covalent geometry    : angle       0.70134 ( 6358)
  Misc. bond           : bond        0.14987 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4552.09 seconds
wall clock time: 80 minutes 35.25 seconds (4835.25 seconds total)