Starting phenix.real_space_refine
on Tue Feb  3 15:50:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lkm_63182/02_2026/9lkm_63182.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lkm_63182/02_2026/9lkm_63182.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lkm_63182/02_2026/9lkm_63182.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lkm_63182/02_2026/9lkm_63182.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lkm_63182/02_2026/9lkm_63182.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lkm_63182/02_2026/9lkm_63182.map"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
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
     Ca      3      9.91       5
     S      25      5.16       5
     C    2819      2.51       5
     N     739      2.21       5
     O     859      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4445
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1017
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 128}
    Chain: "B"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1017
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 128}
    Chain: "C"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 108}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1333
          Classifications: {'peptide': 164}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 157}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "H"
      Number of atoms: 206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 206
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.06, per 1000 atoms: 0.24
  Number of scatterers: 4445
  At special positions: 0
  Unit cell: (96.48, 62.176, 77.184, 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)
     Ca      3     19.99
     S      25     16.00
     O     859      8.00
     N     739      7.00
     C    2819      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  30 " - pdb=" SG  CYS D  55 " distance=2.08
    Simple disulfide: pdb=" SG  CYS D  80 " - pdb=" SG  CYS D 112 " distance=2.01
    Simple disulfide: pdb=" SG  CYS D 168 " - pdb=" SG  CYS D 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 172 " - pdb=" SG  CYS D 198 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D 178 " - pdb=" SG  CYS D 189 " distance=2.03

  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=0, symmetry=0
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 151.3 milliseconds
  

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1030

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 11 sheets defined
      7.7% alpha, 46.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'D' and resid 44 through 48
    Processing helix  chain 'D' and resid 78 through 83
    Processing helix  chain 'D' and resid 96 through 101
    Processing helix  chain 'D' and resid 102 through 105
    Processing helix  chain 'D' and resid 146 through 150
    Processing helix  chain 'D' and resid 164 through 181
      removed outlier: 3.534A  pdb=" N   LYS D 180 " --> pdb=" O   GLU D 176 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 155
      removed outlier: 6.829A  pdb=" N   TYR A 133 " --> pdb=" O   VAL A 152 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ASN A 154 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ALA A 131 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   THR A 173 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 155
      removed outlier: 6.829A  pdb=" N   TYR A 133 " --> pdb=" O   VAL A 152 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ASN A 154 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ALA A 131 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   THR A 173 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU A 181 " --> pdb=" O   HIS A 240 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 145
      removed outlier: 3.747A  pdb=" N   GLU A 144 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LYS A 196 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   VAL A 200 " --> pdb=" O   LYS A 196 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 155
      removed outlier: 4.981A  pdb=" N   VAL B 151 " --> pdb=" O   GLY B 135 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   GLY B 135 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA B 131 " --> pdb=" O   LEU B 155 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   THR B 173 " --> pdb=" O   ILE B 255 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 160
      removed outlier: 3.701A  pdb=" N   LYS B 165 " --> pdb=" O   ASP B 160 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LYS B 196 " --> pdb=" O   GLN B 199 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLN B 199 " --> pdb=" O   LYS B 196 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 160
      removed outlier: 3.701A  pdb=" N   LYS B 165 " --> pdb=" O   ASP B 160 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 153
      removed outlier: 6.806A  pdb=" N   TYR C 133 " --> pdb=" O   VAL C 152 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   THR C 173 " --> pdb=" O   ILE C 255 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASP C 214 " --> pdb=" O   MET C 182 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 145 through 146
      removed outlier: 4.634A  pdb=" N   ILE C 232 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS C 165 " --> pdb=" O   ASP C 160 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 146
      removed outlier: 4.634A  pdb=" N   ILE C 232 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE C 231 " --> pdb=" O   CYS H 195 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   TRP H 191 " --> pdb=" O   ASP C 235 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   LYS H 196 " --> pdb=" O   VAL H 200 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   VAL H 200 " --> pdb=" O   LYS H 196 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 31 through 34
      removed outlier: 6.079A  pdb=" N   THR D  32 " --> pdb=" O   THR D  58 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   GLU D  60 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   VAL D  34 " --> pdb=" O   GLU D  60 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 42
      removed outlier: 3.515A  pdb=" N   VAL D 119 " --> pdb=" O   PHE D  73 " (cutoff:3.500A)

    185 hydrogen bonds defined for protein.
    489 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.39

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1147
        1.33 -     1.45: 1039
        1.45 -     1.58: 2329
        1.58 -     1.70: 0
        1.70 -     1.82: 34
  Bond restraints: 4549
  Sorted by residual:
  bond pdb=" C   LEU D  85 "
       pdb=" O   LEU D  85 "
    ideal  model  delta    sigma   weight residual
    1.235  1.299 -0.064 1.18e-02 7.18e+03 2.97e+01
  bond pdb=" CA  SER D 188 "
       pdb=" CB  SER D 188 "
    ideal  model  delta    sigma   weight residual
    1.523  1.472  0.051 1.35e-02 5.49e+03 1.45e+01
  bond pdb=" N   GLN D  89 "
       pdb=" CA  GLN D  89 "
    ideal  model  delta    sigma   weight residual
    1.454  1.498 -0.044 1.21e-02 6.83e+03 1.35e+01
  bond pdb=" N   LEU D  85 "
       pdb=" CA  LEU D  85 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.20e-02 6.94e+03 1.15e+01
  bond pdb=" C   GLN D  89 "
       pdb=" O   GLN D  89 "
    ideal  model  delta    sigma   weight residual
    1.233  1.275 -0.042 1.28e-02 6.10e+03 1.08e+01
  ... (remaining 4544 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 5213
        1.62 -     3.24: 781
        3.24 -     4.86: 124
        4.86 -     6.48: 22
        6.48 -     8.09: 8
  Bond angle restraints: 6148
  Sorted by residual:
  angle pdb=" N   VAL D 170 "
        pdb=" CA  VAL D 170 "
        pdb=" C   VAL D 170 "
      ideal   model   delta    sigma   weight residual
     110.53  104.63    5.90 9.40e-01 1.13e+00 3.94e+01
  angle pdb=" N   ASN B 169 "
        pdb=" CA  ASN B 169 "
        pdb=" C   ASN B 169 "
      ideal   model   delta    sigma   weight residual
     114.31  106.62    7.69 1.29e+00 6.01e-01 3.56e+01
  angle pdb=" CA  GLN D  89 "
        pdb=" C   GLN D  89 "
        pdb=" O   GLN D  89 "
      ideal   model   delta    sigma   weight residual
     121.72  115.46    6.26 1.18e+00 7.18e-01 2.81e+01
  angle pdb=" N   LYS D 104 "
        pdb=" CA  LYS D 104 "
        pdb=" C   LYS D 104 "
      ideal   model   delta    sigma   weight residual
     111.75  105.40    6.35 1.28e+00 6.10e-01 2.46e+01
  angle pdb=" C   CYS D  30 "
        pdb=" CA  CYS D  30 "
        pdb=" CB  CYS D  30 "
      ideal   model   delta    sigma   weight residual
     110.19  102.10    8.09 1.64e+00 3.72e-01 2.44e+01
  ... (remaining 6143 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.95: 2372
       15.95 -    31.89: 200
       31.89 -    47.84: 47
       47.84 -    63.78: 15
       63.78 -    79.73: 1
  Dihedral angle restraints: 2635
    sinusoidal: 1010
      harmonic: 1625
  Sorted by residual:
  dihedral pdb=" CB  CYS D 172 "
           pdb=" SG  CYS D 172 "
           pdb=" SG  CYS D 198 "
           pdb=" CB  CYS D 198 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.81   53.81     1      1.00e+01 1.00e-02 3.93e+01
  dihedral pdb=" C   CYS D  30 "
           pdb=" N   CYS D  30 "
           pdb=" CA  CYS D  30 "
           pdb=" CB  CYS D  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.00  -14.60     0      2.50e+00 1.60e-01 3.41e+01
  dihedral pdb=" N   CYS D  30 "
           pdb=" C   CYS D  30 "
           pdb=" CA  CYS D  30 "
           pdb=" CB  CYS D  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  108.60   14.20     0      2.50e+00 1.60e-01 3.23e+01
  ... (remaining 2632 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 551
       0.098 -    0.197: 78
       0.197 -    0.295: 12
       0.295 -    0.394: 0
       0.394 -    0.492: 1
  Chirality restraints: 642
  Sorted by residual:
  chirality pdb=" CA  CYS D  30 "
            pdb=" N   CYS D  30 "
            pdb=" C   CYS D  30 "
            pdb=" CB  CYS D  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.00   -0.49 2.00e-01 2.50e+01 6.05e+00
  chirality pdb=" CA  GLN D  89 "
            pdb=" N   GLN D  89 "
            pdb=" C   GLN D  89 "
            pdb=" CB  GLN D  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  LEU D 121 "
            pdb=" N   LEU D 121 "
            pdb=" C   LEU D 121 "
            pdb=" CB  LEU D 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.59e+00
  ... (remaining 639 not shown)

  Planarity restraints: 806
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 131 "   -0.428 9.50e-02 1.11e+02   1.92e-01 2.25e+01
        pdb=" NE  ARG D 131 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 131 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 131 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 131 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D  91 "   -0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   ASP D  91 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ASP D  91 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   HIS D  92 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 127 "   -0.057 5.00e-02 4.00e+02   8.47e-02 1.15e+01
        pdb=" N   PRO B 128 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO B 128 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B 128 "   -0.047 5.00e-02 4.00e+02
  ... (remaining 803 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1493
        2.83 -     3.35: 3934
        3.35 -     3.86: 7367
        3.86 -     4.38: 8638
        4.38 -     4.90: 14934
  Nonbonded interactions: 36366
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS B 223 "
            pdb=" OD2 ASP B 258 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" OE1 GLN C 211 "
            pdb=" OH  TYR C 213 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" O   ILE A 170 "
            pdb=" OH  TYR A 174 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" O   ILE C 170 "
            pdb=" OH  TYR C 174 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" N   ASN A 243 "
            pdb=" OD1 ASN A 243 "
     model   vdw
     2.357 3.120
  ... (remaining 36361 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 127 through 258)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.880
  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:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     4.850
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6521
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   0.064   4554  Z= 0.631
  Angle     :  1.198  10.272   6158  Z= 0.843
  Chirality :  0.073   0.492    642
  Planarity :  0.011   0.192    806
  Dihedral  : 13.088  79.727   1590
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 31.72
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  8.68 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  :  4.64 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.09 (0.30), residues: 553
  helix: -3.73 (0.53), residues: 25
  sheet: -0.84 (0.33), residues: 218
  loop : -2.94 (0.27), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 131 
 TYR   0.016   0.001   TYR D  70 
 PHE   0.022   0.002   PHE D  73 
 TRP   0.010   0.002   TRP D  57 
 HIS   0.005   0.001   HIS D  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00869 ( 4549)
  covalent geometry    : angle       1.18928 ( 6148)
  SS BOND              : bond        0.02652 (    5)
  SS BOND              : angle       3.83263 (   10)
  hydrogen bonds       : bond        0.19773 (  163)
  hydrogen bonds       : angle       8.70107 (  489)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 TYR cc_start: 0.7356 (m-80) cc_final: 0.6740 (m-80)
REVERT: D   45 SER cc_start: 0.8007 (t) cc_final: 0.7759 (p)
REVERT: D   62 PRO cc_start: 0.8000 (Cg_exo) cc_final: 0.7563 (Cg_endo)
REVERT: D   63 ASP cc_start: 0.7761 (t0) cc_final: 0.7479 (t70)
REVERT: D   67 TYR cc_start: 0.8069 (m-80) cc_final: 0.7780 (m-10)
REVERT: D   73 PHE cc_start: 0.5995 (OUTLIER) cc_final: 0.5727 (m-80)
REVERT: D  125 LYS cc_start: 0.8045 (mttm) cc_final: 0.7576 (mttm)
  outliers start: 14
  outliers final: 6
  residues processed: 147
  average time/residue: 0.0718
  time to fit residues: 13.1756
Evaluate side-chains
  137 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 130
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   47 MET
Chi-restraints excluded: chain D residue   73 PHE
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue  113 ASN
Chi-restraints excluded: chain D residue  151 SER
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain D residue  196 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0970
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.3980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
B 138 ASN
B 211 GLN
C 158 ASN
D 105 ASN
D 110 GLN
D 113 ASN
D 129 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.155527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.133453 restraints weight = 6573.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.98
r_work: 0.3583 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4554  Z= 0.166
  Angle     :  0.622   6.435   6158  Z= 0.343
  Chirality :  0.044   0.139    642
  Planarity :  0.004   0.030    806
  Dihedral  :  6.419  55.031    624
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 13.08 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.32), residues: 553
  helix: -2.22 (0.76), residues: 33
  sheet: -0.39 (0.33), residues: 219
  loop : -2.11 (0.31), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 131 
 TYR   0.015   0.002   TYR D  67 
 PHE   0.022   0.002   PHE A 250 
 TRP   0.011   0.002   TRP D 174 
 HIS   0.006   0.001   HIS D 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 4549)
  covalent geometry    : angle       0.61860 ( 6148)
  SS BOND              : bond        0.00555 (    5)
  SS BOND              : angle       1.63884 (   10)
  hydrogen bonds       : bond        0.04701 (  163)
  hydrogen bonds       : angle       6.58737 (  489)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ARG cc_start: 0.7874 (mmp80) cc_final: 0.7574 (mmt-90)
REVERT: A  207 GLN cc_start: 0.8131 (tt0) cc_final: 0.7807 (tt0)
REVERT: C  181 LEU cc_start: 0.6770 (tp) cc_final: 0.6414 (tp)
REVERT: C  212 ASN cc_start: 0.5676 (m-40) cc_final: 0.5366 (m-40)
REVERT: C  218 ASN cc_start: 0.8018 (t0) cc_final: 0.7817 (t0)
REVERT: C  232 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7787 (mt)
REVERT: D   45 SER cc_start: 0.8382 (t) cc_final: 0.8171 (p)
REVERT: D  159 ASN cc_start: 0.7609 (t0) cc_final: 0.7302 (t0)
REVERT: H  190 MET cc_start: 0.7564 (ttt) cc_final: 0.7329 (ttt)
  outliers start: 17
  outliers final: 11
  residues processed: 133
  average time/residue: 0.0618
  time to fit residues: 10.2899
Evaluate side-chains
  133 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   41 SER
Chi-restraints excluded: chain D residue   47 MET
Chi-restraints excluded: chain D residue  151 SER
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  179 LEU
Chi-restraints excluded: chain D residue  196 CYS
Chi-restraints excluded: chain H residue  189 SER
Chi-restraints excluded: chain H residue  205 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0060
   chunk 17 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
D 122 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.154375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.132208 restraints weight = 6431.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.96
r_work: 0.3550 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.3740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4554  Z= 0.167
  Angle     :  0.588   6.718   6158  Z= 0.319
  Chirality :  0.044   0.142    642
  Planarity :  0.003   0.032    806
  Dihedral  :  5.751  59.478    618
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.46 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.33), residues: 553
  helix: -0.92 (0.82), residues: 34
  sheet:  0.18 (0.35), residues: 213
  loop : -2.05 (0.30), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D 132 
 TYR   0.019   0.002   TYR C 247 
 PHE   0.023   0.002   PHE D 134 
 TRP   0.010   0.002   TRP B 191 
 HIS   0.005   0.001   HIS D 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 4549)
  covalent geometry    : angle       0.58615 ( 6148)
  SS BOND              : bond        0.00453 (    5)
  SS BOND              : angle       1.33897 (   10)
  hydrogen bonds       : bond        0.04374 (  163)
  hydrogen bonds       : angle       6.21947 (  489)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ARG cc_start: 0.8002 (mmp80) cc_final: 0.7741 (mmt-90)
REVERT: A  207 GLN cc_start: 0.8251 (tt0) cc_final: 0.7973 (tt0)
REVERT: B  182 MET cc_start: 0.7373 (ttp) cc_final: 0.7048 (ttt)
REVERT: C  181 LEU cc_start: 0.6954 (tp) cc_final: 0.6617 (tp)
REVERT: C  212 ASN cc_start: 0.6225 (m-40) cc_final: 0.5867 (m-40)
REVERT: C  218 ASN cc_start: 0.8126 (t0) cc_final: 0.7887 (t0)
REVERT: C  232 ILE cc_start: 0.8241 (mm) cc_final: 0.8002 (mt)
REVERT: D  159 ASN cc_start: 0.7862 (t0) cc_final: 0.7569 (t0)
  outliers start: 15
  outliers final: 7
  residues processed: 130
  average time/residue: 0.0715
  time to fit residues: 11.6786
Evaluate side-chains
  128 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 121
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain H residue  189 SER
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  205 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   chunk 44 optimal weight:    0.0670
   chunk 28 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5920

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.153380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.131230 restraints weight = 6443.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.96
r_work: 0.3534 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.4353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4554  Z= 0.165
  Angle     :  0.580   6.348   6158  Z= 0.310
  Chirality :  0.043   0.161    642
  Planarity :  0.003   0.032    806
  Dihedral  :  4.541  14.384    611
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.72 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.34), residues: 553
  helix: -0.62 (0.82), residues: 34
  sheet:  0.34 (0.33), residues: 241
  loop : -2.17 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 131 
 TYR   0.022   0.002   TYR D  88 
 PHE   0.023   0.002   PHE D 134 
 TRP   0.010   0.002   TRP B 191 
 HIS   0.005   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 4549)
  covalent geometry    : angle       0.57757 ( 6148)
  SS BOND              : bond        0.00434 (    5)
  SS BOND              : angle       1.41941 (   10)
  hydrogen bonds       : bond        0.04094 (  163)
  hydrogen bonds       : angle       6.05285 (  489)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A  201 ARG cc_start: 0.8090 (mmp80) cc_final: 0.7732 (mmt-90)
REVERT: A  207 GLN cc_start: 0.8334 (tt0) cc_final: 0.8018 (tt0)
REVERT: B  182 MET cc_start: 0.7403 (ttp) cc_final: 0.7082 (ttt)
REVERT: C  154 ASN cc_start: 0.8084 (t0) cc_final: 0.7869 (t0)
REVERT: C  181 LEU cc_start: 0.6966 (tp) cc_final: 0.6604 (tp)
REVERT: C  212 ASN cc_start: 0.6483 (m-40) cc_final: 0.6081 (m-40)
REVERT: D  159 ASN cc_start: 0.7987 (t0) cc_final: 0.7686 (t0)
REVERT: D  175 LEU cc_start: 0.7966 (mp) cc_final: 0.7615 (mt)
  outliers start: 19
  outliers final: 14
  residues processed: 124
  average time/residue: 0.0648
  time to fit residues: 9.9879
Evaluate side-chains
  131 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  196 LYS
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain D residue   83 PHE
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LYS
Chi-restraints excluded: chain H residue  189 SER
Chi-restraints excluded: chain H residue  199 GLN
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  205 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0070
   chunk 22 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
B 212 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.152264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.130193 restraints weight = 6439.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.92
r_work: 0.3524 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.4749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4554  Z= 0.166
  Angle     :  0.566   6.426   6158  Z= 0.304
  Chirality :  0.043   0.176    642
  Planarity :  0.003   0.031    806
  Dihedral  :  4.468  14.380    611
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 18.14 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.34), residues: 553
  helix: -0.03 (0.91), residues: 34
  sheet:  0.43 (0.33), residues: 243
  loop : -2.21 (0.32), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 132 
 TYR   0.014   0.001   TYR D  39 
 PHE   0.026   0.002   PHE D 134 
 TRP   0.009   0.002   TRP B 191 
 HIS   0.005   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4549)
  covalent geometry    : angle       0.56342 ( 6148)
  SS BOND              : bond        0.00589 (    5)
  SS BOND              : angle       1.38700 (   10)
  hydrogen bonds       : bond        0.04086 (  163)
  hydrogen bonds       : angle       5.95980 (  489)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8501 (mttp) cc_final: 0.8195 (mttp)
REVERT: A  201 ARG cc_start: 0.8151 (mmp80) cc_final: 0.7844 (mmt-90)
REVERT: A  207 GLN cc_start: 0.8316 (tt0) cc_final: 0.7995 (tt0)
REVERT: A  256 TYR cc_start: 0.8521 (m-10) cc_final: 0.8246 (m-10)
REVERT: B  182 MET cc_start: 0.7436 (ttp) cc_final: 0.7111 (ttt)
REVERT: C  181 LEU cc_start: 0.6958 (tp) cc_final: 0.6757 (tp)
REVERT: C  212 ASN cc_start: 0.6454 (m-40) cc_final: 0.6040 (m-40)
REVERT: D   88 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6413 (p90)
REVERT: D  109 MET cc_start: 0.6700 (tmm) cc_final: 0.6265 (tmm)
REVERT: D  159 ASN cc_start: 0.8003 (t0) cc_final: 0.7713 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 130
  average time/residue: 0.0564
  time to fit residues: 9.2393
Evaluate side-chains
  130 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  196 LYS
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain D residue   83 PHE
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LYS
Chi-restraints excluded: chain H residue  189 SER
Chi-restraints excluded: chain H residue  199 GLN
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  205 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 38 optimal weight:    0.3980
   chunk 27 optimal weight:    0.0570
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.5900

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

Flipped N/Q/H residues before XYZ refinement:
B 212 ASN
D 129 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.151286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.129122 restraints weight = 6622.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.97
r_work: 0.3514 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.5029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4554  Z= 0.166
  Angle     :  0.580   7.346   6158  Z= 0.309
  Chirality :  0.044   0.201    642
  Planarity :  0.003   0.031    806
  Dihedral  :  4.470  13.844    611
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.99 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.34), residues: 553
  helix: -0.39 (0.83), residues: 41
  sheet:  0.49 (0.33), residues: 239
  loop : -2.12 (0.32), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 129 
 TYR   0.015   0.001   TYR D  39 
 PHE   0.027   0.002   PHE D 134 
 TRP   0.010   0.002   TRP A 191 
 HIS   0.005   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4549)
  covalent geometry    : angle       0.57810 ( 6148)
  SS BOND              : bond        0.00387 (    5)
  SS BOND              : angle       1.22142 (   10)
  hydrogen bonds       : bond        0.03941 (  163)
  hydrogen bonds       : angle       5.92315 (  489)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8529 (mttp) cc_final: 0.8214 (mttp)
REVERT: A  201 ARG cc_start: 0.8167 (mmp80) cc_final: 0.7875 (mmt-90)
REVERT: A  207 GLN cc_start: 0.8316 (tt0) cc_final: 0.7998 (tt0)
REVERT: A  256 TYR cc_start: 0.8633 (m-10) cc_final: 0.8226 (m-10)
REVERT: B  182 MET cc_start: 0.7477 (ttp) cc_final: 0.7147 (ttt)
REVERT: C  154 ASN cc_start: 0.8060 (t0) cc_final: 0.7844 (t0)
REVERT: C  212 ASN cc_start: 0.6511 (m-40) cc_final: 0.6200 (m-40)
REVERT: D  109 MET cc_start: 0.6688 (tmm) cc_final: 0.6297 (tmm)
REVERT: D  159 ASN cc_start: 0.8057 (t0) cc_final: 0.7838 (t0)
REVERT: D  162 SER cc_start: 0.7278 (p) cc_final: 0.6784 (p)
  outliers start: 19
  outliers final: 16
  residues processed: 124
  average time/residue: 0.0582
  time to fit residues: 9.0172
Evaluate side-chains
  131 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  196 LYS
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain D residue   83 PHE
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LYS
Chi-restraints excluded: chain H residue  189 SER
Chi-restraints excluded: chain H residue  199 GLN
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  205 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0870
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0470
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.3856

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

Flipped N/Q/H residues before XYZ refinement:
B 212 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.153161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.131477 restraints weight = 6499.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 2.82
r_work: 0.3547 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4554  Z= 0.125
  Angle     :  0.549   6.731   6158  Z= 0.290
  Chirality :  0.043   0.215    642
  Planarity :  0.003   0.030    806
  Dihedral  :  4.271  13.358    611
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 21.31 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.34), residues: 553
  helix: -0.07 (0.85), residues: 41
  sheet:  0.54 (0.34), residues: 242
  loop : -2.14 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 131 
 TYR   0.016   0.001   TYR D  39 
 PHE   0.028   0.002   PHE D 134 
 TRP   0.006   0.001   TRP B 191 
 HIS   0.005   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4549)
  covalent geometry    : angle       0.54823 ( 6148)
  SS BOND              : bond        0.00263 (    5)
  SS BOND              : angle       0.83472 (   10)
  hydrogen bonds       : bond        0.03440 (  163)
  hydrogen bonds       : angle       5.67602 (  489)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8527 (mttp) cc_final: 0.8222 (mttp)
REVERT: A  201 ARG cc_start: 0.8152 (mmp80) cc_final: 0.7886 (mmt-90)
REVERT: A  207 GLN cc_start: 0.8291 (tt0) cc_final: 0.8035 (tt0)
REVERT: A  256 TYR cc_start: 0.8610 (m-10) cc_final: 0.8275 (m-10)
REVERT: B  182 MET cc_start: 0.7404 (ttp) cc_final: 0.7084 (ttt)
REVERT: C  212 ASN cc_start: 0.6412 (m-40) cc_final: 0.6152 (m-40)
REVERT: D  109 MET cc_start: 0.6586 (tmm) cc_final: 0.6250 (tmm)
REVERT: D  162 SER cc_start: 0.7365 (p) cc_final: 0.6972 (p)
  outliers start: 16
  outliers final: 13
  residues processed: 122
  average time/residue: 0.0585
  time to fit residues: 8.9394
Evaluate side-chains
  129 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  229 GLU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  180 LYS
Chi-restraints excluded: chain H residue  189 SER
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  205 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0060
   chunk 20 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0040
   overall best weight:    0.4808

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.152408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.130095 restraints weight = 6500.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.98
r_work: 0.3523 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.5336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4554  Z= 0.144
  Angle     :  0.566   7.149   6158  Z= 0.300
  Chirality :  0.044   0.249    642
  Planarity :  0.003   0.030    806
  Dihedral  :  4.282  13.381    611
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.57 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.34), residues: 553
  helix: -0.01 (0.86), residues: 41
  sheet:  0.61 (0.34), residues: 239
  loop : -2.07 (0.32), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 129 
 TYR   0.015   0.001   TYR D  39 
 PHE   0.029   0.002   PHE D 134 
 TRP   0.008   0.001   TRP A 191 
 HIS   0.004   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4549)
  covalent geometry    : angle       0.56516 ( 6148)
  SS BOND              : bond        0.00265 (    5)
  SS BOND              : angle       0.76024 (   10)
  hydrogen bonds       : bond        0.03584 (  163)
  hydrogen bonds       : angle       5.70689 (  489)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8526 (mttp) cc_final: 0.8220 (mttp)
REVERT: A  201 ARG cc_start: 0.8179 (mmp80) cc_final: 0.7908 (mmt-90)
REVERT: A  207 GLN cc_start: 0.8274 (tt0) cc_final: 0.8026 (tt0)
REVERT: A  256 TYR cc_start: 0.8675 (m-10) cc_final: 0.8439 (m-80)
REVERT: B  182 MET cc_start: 0.7448 (ttp) cc_final: 0.7115 (ttt)
REVERT: C  146 LEU cc_start: 0.8467 (mp) cc_final: 0.8210 (mt)
REVERT: D  109 MET cc_start: 0.6626 (tmm) cc_final: 0.6279 (tmm)
REVERT: D  162 SER cc_start: 0.7465 (p) cc_final: 0.7235 (p)
  outliers start: 16
  outliers final: 14
  residues processed: 121
  average time/residue: 0.0787
  time to fit residues: 11.6570
Evaluate side-chains
  128 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain D residue   63 ASP
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LYS
Chi-restraints excluded: chain H residue  189 SER
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  205 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0570
   chunk 24 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
D  92 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.151533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.129298 restraints weight = 6501.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.96
r_work: 0.3509 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.5557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4554  Z= 0.185
  Angle     :  0.613   7.527   6158  Z= 0.325
  Chirality :  0.044   0.257    642
  Planarity :  0.003   0.031    806
  Dihedral  :  4.517  14.362    611
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.94 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.34), residues: 553
  helix: -0.13 (0.84), residues: 41
  sheet:  0.55 (0.34), residues: 235
  loop : -2.06 (0.32), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 183 
 TYR   0.016   0.002   TYR B 256 
 PHE   0.029   0.002   PHE D 134 
 TRP   0.010   0.002   TRP B 191 
 HIS   0.005   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 4549)
  covalent geometry    : angle       0.61265 ( 6148)
  SS BOND              : bond        0.00253 (    5)
  SS BOND              : angle       0.76112 (   10)
  hydrogen bonds       : bond        0.03972 (  163)
  hydrogen bonds       : angle       5.90901 (  489)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  201 ARG cc_start: 0.8193 (mmp80) cc_final: 0.7883 (mmt-90)
REVERT: A  207 GLN cc_start: 0.8298 (tt0) cc_final: 0.7946 (tt0)
REVERT: A  256 TYR cc_start: 0.8684 (m-10) cc_final: 0.8313 (m-10)
REVERT: B  178 TYR cc_start: 0.8568 (p90) cc_final: 0.7943 (p90)
REVERT: B  182 MET cc_start: 0.7475 (ttp) cc_final: 0.7135 (ttt)
REVERT: B  233 LYS cc_start: 0.7747 (tmtt) cc_final: 0.7535 (tmtt)
REVERT: C  181 LEU cc_start: 0.6991 (tp) cc_final: 0.6703 (tp)
REVERT: C  224 LEU cc_start: 0.8201 (mt) cc_final: 0.7999 (mp)
REVERT: D  109 MET cc_start: 0.6580 (tmm) cc_final: 0.6247 (tmm)
REVERT: D  162 SER cc_start: 0.7487 (p) cc_final: 0.7199 (p)
REVERT: D  197 THR cc_start: 0.7777 (m) cc_final: 0.7558 (m)
  outliers start: 17
  outliers final: 15
  residues processed: 120
  average time/residue: 0.0878
  time to fit residues: 13.0115
Evaluate side-chains
  126 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  229 GLU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain D residue   83 PHE
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LYS
Chi-restraints excluded: chain H residue  189 SER
Chi-restraints excluded: chain H residue  199 GLN
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  205 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.151875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.129139 restraints weight = 6422.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.98
r_work: 0.3511 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.5711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4554  Z= 0.184
  Angle     :  0.618   7.328   6158  Z= 0.329
  Chirality :  0.044   0.248    642
  Planarity :  0.004   0.070    806
  Dihedral  :  4.527  14.583    611
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 23.21 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.34), residues: 553
  helix: -0.21 (0.84), residues: 41
  sheet:  0.49 (0.34), residues: 235
  loop : -2.07 (0.32), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 201 
 TYR   0.014   0.002   TYR D  39 
 PHE   0.030   0.002   PHE D 134 
 TRP   0.009   0.001   TRP B 191 
 HIS   0.005   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 4549)
  covalent geometry    : angle       0.61782 ( 6148)
  SS BOND              : bond        0.00246 (    5)
  SS BOND              : angle       0.76359 (   10)
  hydrogen bonds       : bond        0.03892 (  163)
  hydrogen bonds       : angle       5.90480 (  489)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  147 LYS cc_start: 0.8461 (mttp) cc_final: 0.8184 (mttp)
REVERT: A  201 ARG cc_start: 0.8192 (mmp80) cc_final: 0.7891 (mmt-90)
REVERT: A  207 GLN cc_start: 0.8296 (tt0) cc_final: 0.7942 (tt0)
REVERT: A  256 TYR cc_start: 0.8687 (m-10) cc_final: 0.8320 (m-10)
REVERT: B  178 TYR cc_start: 0.8574 (p90) cc_final: 0.7906 (p90)
REVERT: B  182 MET cc_start: 0.7483 (ttp) cc_final: 0.7266 (ttt)
REVERT: B  233 LYS cc_start: 0.7763 (tmtt) cc_final: 0.7541 (tmtt)
REVERT: C  181 LEU cc_start: 0.6982 (tp) cc_final: 0.6696 (tp)
REVERT: C  224 LEU cc_start: 0.8215 (mt) cc_final: 0.8003 (mp)
REVERT: D  109 MET cc_start: 0.6581 (tmm) cc_final: 0.6221 (tmm)
REVERT: D  162 SER cc_start: 0.7471 (p) cc_final: 0.7262 (p)
REVERT: D  197 THR cc_start: 0.7736 (m) cc_final: 0.7514 (m)
  outliers start: 15
  outliers final: 14
  residues processed: 126
  average time/residue: 0.0805
  time to fit residues: 12.6177
Evaluate side-chains
  133 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain D residue   83 PHE
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LYS
Chi-restraints excluded: chain H residue  189 SER
Chi-restraints excluded: chain H residue  199 GLN
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  205 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0170
   chunk 31 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.6018

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.152133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.129495 restraints weight = 6467.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.97
r_work: 0.3512 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.5826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4554  Z= 0.172
  Angle     :  0.615   7.500   6158  Z= 0.326
  Chirality :  0.044   0.237    642
  Planarity :  0.004   0.058    806
  Dihedral  :  4.533  14.885    611
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 23.63 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.34), residues: 553
  helix: -0.19 (0.84), residues: 41
  sheet:  0.42 (0.34), residues: 237
  loop : -2.13 (0.32), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 183 
 TYR   0.014   0.001   TYR D  39 
 PHE   0.029   0.002   PHE D 134 
 TRP   0.008   0.001   TRP B 191 
 HIS   0.004   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 4549)
  covalent geometry    : angle       0.61531 ( 6148)
  SS BOND              : bond        0.00197 (    5)
  SS BOND              : angle       0.66187 (   10)
  hydrogen bonds       : bond        0.03805 (  163)
  hydrogen bonds       : angle       5.84611 (  489)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1046.65 seconds
wall clock time: 18 minutes 38.07 seconds (1118.07 seconds total)