Starting phenix.real_space_refine
on Tue Feb  3 12:33:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cwq_45971/02_2026/9cwq_45971.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cwq_45971/02_2026/9cwq_45971.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cwq_45971/02_2026/9cwq_45971.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cwq_45971/02_2026/9cwq_45971.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cwq_45971/02_2026/9cwq_45971.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cwq_45971/02_2026/9cwq_45971.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.051
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: 4
    Type Number    sf(0)   Gaussians
     S       8      5.16       5
     C    1315      2.51       5
     N     315      2.21       5
     O     376      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 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: 2014
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1888
          Classifications: {'peptide': 248}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 13, 'TRANS': 234}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 69
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 0.76, per 1000 atoms: 0.38
  Number of scatterers: 2014
  At special positions: 0
  Unit cell: (59, 63, 73, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       8     16.00
     O     376      8.00
     N     315      7.00
     C    1315      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.18
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.01

  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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 401 " - " ASN A 234 "
      " NAG A 402 " - " ASN A 165 "
      " NAG A 403 " - " ASN A  62 "
      " NAG B   1 " - " ASN A 282 "
      " NAG C   1 " - " ASN A 245 "
      " NAG D   1 " - " ASN A 122 "
  Time building additional restraints: 0.16
  Conformation dependent library (CDL) restraints added in 47.4 milliseconds
  

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  474

  Finding SS restraints...
    Secondary structure from input PDB file:
      1 helices and 4 sheets defined
      4.0% alpha, 66.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 303
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 31
      removed outlier: 8.200A  pdb=" N   ASN A  62 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   ASP A 228 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 56
      removed outlier: 7.390A  pdb=" N   THR A 274 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   ASP A 290 " --> pdb=" O   THR A 274 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LEU A 276 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ALA A 288 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   LYS A 278 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.722A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE A 168 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   GLU A 132 " --> pdb=" O   CYS A 166 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   CYS A 166 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   GLN A 134 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 8.677A  pdb=" N   ASN A 164 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   CYS A 136 " --> pdb=" O   SER A 162 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   SER A 162 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 10.770A  pdb=" N   ASP A 138 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   TYR A 160 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85
      removed outlier: 12.976A  pdb=" N   PHE A 238 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 13.116A  pdb=" N   PHE A 135 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
      removed outlier: 13.524A  pdb=" N   THR A 240 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 11.795A  pdb=" N   ASN A 137 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 10.773A  pdb=" N   LEU A 242 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
      removed outlier: 8.192A  pdb=" N   LEU A 244 " --> pdb=" O   PRO A 139 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE A 168 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   GLU A 132 " --> pdb=" O   CYS A 166 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   CYS A 166 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   GLN A 134 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 8.677A  pdb=" N   ASN A 164 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   CYS A 136 " --> pdb=" O   SER A 162 " (cutoff:3.500A)
      removed outlier: 9.878A  pdb=" N   SER A 162 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 10.770A  pdb=" N   ASP A 138 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   TYR A 160 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)

    90 hydrogen bonds defined for protein.
    234 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: 0.17

  Time building geometry restraints manager: 0.20 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 337
        1.32 -     1.44: 571
        1.44 -     1.57: 1143
        1.57 -     1.70: 1
        1.70 -     1.82: 10
  Bond restraints: 2062
  Sorted by residual:
  bond pdb=" C   LYS A 129 "
       pdb=" O   LYS A 129 "
    ideal  model  delta    sigma   weight residual
    1.234  1.193  0.040 1.22e-02 6.72e+03 1.10e+01
  bond pdb=" C   PRO A 272 "
       pdb=" O   PRO A 272 "
    ideal  model  delta    sigma   weight residual
    1.235  1.195  0.040 1.30e-02 5.92e+03 9.57e+00
  bond pdb=" N   ILE A 101 "
       pdb=" CA  ILE A 101 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.19e-02 7.06e+03 9.40e+00
  bond pdb=" CB  LEU A  22 "
       pdb=" CG  LEU A  22 "
    ideal  model  delta    sigma   weight residual
    1.530  1.590 -0.060 2.00e-02 2.50e+03 9.11e+00
  bond pdb=" N   ILE A 100 "
       pdb=" CA  ILE A 100 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.036 1.21e-02 6.83e+03 8.64e+00
  ... (remaining 2057 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 2376
        1.69 -     3.39: 336
        3.39 -     5.08: 61
        5.08 -     6.77: 30
        6.77 -     8.46: 4
  Bond angle restraints: 2807
  Sorted by residual:
  angle pdb=" C   PHE A 216 "
        pdb=" N   PRO A 217 "
        pdb=" CA  PRO A 217 "
      ideal   model   delta    sigma   weight residual
     120.03  127.46   -7.43 9.90e-01 1.02e+00 5.64e+01
  angle pdb=" C   ASP A 294 "
        pdb=" N   PRO A 295 "
        pdb=" CA  PRO A 295 "
      ideal   model   delta    sigma   weight residual
     119.56  126.63   -7.07 1.02e+00 9.61e-01 4.81e+01
  angle pdb=" C   ASN A  81 "
        pdb=" N   PRO A  82 "
        pdb=" CA  PRO A  82 "
      ideal   model   delta    sigma   weight residual
     120.03  126.56   -6.53 9.90e-01 1.02e+00 4.35e+01
  angle pdb=" C   TYR A  39 "
        pdb=" N   PRO A  40 "
        pdb=" CA  PRO A  40 "
      ideal   model   delta    sigma   weight residual
     119.56  126.18   -6.62 1.01e+00 9.80e-01 4.30e+01
  angle pdb=" C   GLU A 224 "
        pdb=" N   PRO A 225 "
        pdb=" CA  PRO A 225 "
      ideal   model   delta    sigma   weight residual
     119.93  126.26   -6.33 1.07e+00 8.73e-01 3.50e+01
  ... (remaining 2802 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.86: 1243
       16.86 -    33.71: 51
       33.71 -    50.57: 12
       50.57 -    67.42: 8
       67.42 -    84.28: 3
  Dihedral angle restraints: 1317
    sinusoidal: 590
      harmonic: 727
  Sorted by residual:
  dihedral pdb=" CB  LYS A  97 "
           pdb=" CG  LYS A  97 "
           pdb=" CD  LYS A  97 "
           pdb=" CE  LYS A  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.69  -57.69     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CG  LYS A  97 "
           pdb=" CD  LYS A  97 "
           pdb=" CE  LYS A  97 "
           pdb=" NZ  LYS A  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.89   57.11     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" CB  MET A  17 "
           pdb=" CG  MET A  17 "
           pdb=" SD  MET A  17 "
           pdb=" CE  MET A  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.97  -54.03     3      1.50e+01 4.44e-03 9.25e+00
  ... (remaining 1314 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 223
       0.066 -    0.133: 75
       0.133 -    0.199: 32
       0.199 -    0.265: 7
       0.265 -    0.331: 11
  Chirality restraints: 348
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.55    0.15 2.00e-02 2.50e+03 5.79e+01
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.50    0.10 2.00e-02 2.50e+03 2.66e+01
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.50    0.10 2.00e-02 2.50e+03 2.34e+01
  ... (remaining 345 not shown)

  Planarity restraints: 348
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 128 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.77e+00
        pdb=" C   ILE A 128 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ILE A 128 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LYS A 129 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  96 "    0.011 2.00e-02 2.50e+03   2.33e-02 5.43e+00
        pdb=" C   GLU A  96 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   GLU A  96 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LYS A  97 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 210 "    0.011 2.00e-02 2.50e+03   2.30e-02 5.30e+00
        pdb=" C   ILE A 210 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE A 210 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ILE A 212 "    0.014 2.00e-02 2.50e+03
  ... (remaining 345 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 904
        2.94 -     3.43: 1656
        3.43 -     3.92: 3201
        3.92 -     4.41: 3657
        4.41 -     4.90: 6284
  Nonbonded interactions: 15702
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 111 "
            pdb=" NZ  LYS A 113 "
     model   vdw
     2.452 3.120
  nonbonded pdb=" OE2 GLU A  96 "
            pdb=" N   ILE A 100 "
     model   vdw
     2.485 3.120
  nonbonded pdb=" N   SER A  98 "
            pdb=" O   SER A  98 "
     model   vdw
     2.487 2.496
  nonbonded pdb=" O   ASN A 137 "
            pdb=" CA  ASP A 138 "
     model   vdw
     2.565 2.776
  nonbonded pdb=" N   GLY A 158 "
            pdb=" N   VAL A 159 "
     model   vdw
     2.578 2.560
  ... (remaining 15697 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 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.130
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.890
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:5.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
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      :  0.013   0.149   2074  Z= 0.707
  Angle     :  1.396   8.464   2840  Z= 0.879
  Chirality :  0.095   0.331    348
  Planarity :  0.006   0.030    342
  Dihedral  : 11.616  84.280    834
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  :  1.61 %
    Favored  : 95.70 %
  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:  0.53 (0.51), residues: 234
  helix:  0.75 (1.83), residues: 11
  sheet:  1.43 (0.48), residues: 104
  loop : -0.71 (0.50), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 102 
 TYR   0.017   0.003   TYR A 269 
 PHE   0.013   0.003   PHE A 220 
 TRP   0.004   0.002   TRP A 104 
 HIS   0.004   0.002   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.01188 ( 2062)
  covalent geometry    : angle       1.38172 ( 2807)
  SS BOND              : bond        0.08671 (    3)
  SS BOND              : angle       2.38115 (    6)
  hydrogen bonds       : bond        0.14863 (   79)
  hydrogen bonds       : angle      10.92089 (  234)
  link_BETA1-4         : bond        0.06134 (    3)
  link_BETA1-4         : angle       2.67345 (    9)
  link_NAG-ASN         : bond        0.06022 (    6)
  link_NAG-ASN         : angle       2.04926 (   18)

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

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

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.043 
Fit side-chains
REVERT: A   17 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.6273 (mtp)
REVERT: A   97 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6394 (mmtp)
REVERT: A  100 ILE cc_start: 0.8485 (mt) cc_final: 0.8281 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 48
  average time/residue: 0.4140
  time to fit residues: 20.1969
Evaluate side-chains
  36 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  206 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.3980
   chunk 6 optimal weight:    0.5980
   chunk 4 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:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.151879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.121937 restraints weight = 2258.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.04
r_work: 0.3229 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   2074  Z= 0.228
  Angle     :  0.701   8.200   2840  Z= 0.357
  Chirality :  0.047   0.169    348
  Planarity :  0.004   0.027    342
  Dihedral  :  7.487  48.106    460
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  9.68 %
    Favored  : 88.71 %
  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:  0.74 (0.53), residues: 234
  helix:  1.20 (1.68), residues: 11
  sheet:  1.60 (0.47), residues: 107
  loop : -0.70 (0.55), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 273 
 TYR   0.013   0.002   TYR A 265 
 PHE   0.016   0.003   PHE A 275 
 TRP   0.006   0.002   TRP A 104 
 HIS   0.003   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 2062)
  covalent geometry    : angle       0.66743 ( 2807)
  SS BOND              : bond        0.00847 (    3)
  SS BOND              : angle       3.12216 (    6)
  hydrogen bonds       : bond        0.03203 (   79)
  hydrogen bonds       : angle       7.49622 (  234)
  link_BETA1-4         : bond        0.00367 (    3)
  link_BETA1-4         : angle       1.36492 (    9)
  link_NAG-ASN         : bond        0.00338 (    6)
  link_NAG-ASN         : angle       1.95830 (   18)

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

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

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.6647 (mmtp)
REVERT: A  111 ASP cc_start: 0.7749 (p0) cc_final: 0.7484 (p0)
REVERT: A  113 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7530 (mttm)
REVERT: A  190 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8352 (mtm180)
  outliers start: 3
  outliers final: 0
  residues processed: 42
  average time/residue: 0.3597
  time to fit residues: 15.4162
Evaluate side-chains
  38 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  113 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 0 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 15 optimal weight:    0.4980
   chunk 11 optimal weight:    0.0870
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   chunk 9 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.151688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.121904 restraints weight = 2232.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.02
r_work: 0.3259 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   2074  Z= 0.178
  Angle     :  0.612   8.900   2840  Z= 0.315
  Chirality :  0.045   0.161    348
  Planarity :  0.004   0.026    342
  Dihedral  :  5.099  34.184    453
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.29 %
    Favored  : 87.10 %
  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:  0.73 (0.54), residues: 234
  helix:  2.03 (1.67), residues: 11
  sheet:  1.63 (0.49), residues: 105
  loop : -0.80 (0.55), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 273 
 TYR   0.013   0.001   TYR A 265 
 PHE   0.012   0.002   PHE A 127 
 TRP   0.004   0.001   TRP A 104 
 HIS   0.003   0.002   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 2062)
  covalent geometry    : angle       0.59167 ( 2807)
  SS BOND              : bond        0.00954 (    3)
  SS BOND              : angle       1.77623 (    6)
  hydrogen bonds       : bond        0.02927 (   79)
  hydrogen bonds       : angle       7.02641 (  234)
  link_BETA1-4         : bond        0.00514 (    3)
  link_BETA1-4         : angle       1.34083 (    9)
  link_NAG-ASN         : bond        0.00272 (    6)
  link_NAG-ASN         : angle       1.62565 (   18)

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

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

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A   17 MET cc_start: 0.6817 (mmt) cc_final: 0.5040 (ptt)
REVERT: A  111 ASP cc_start: 0.7521 (p0) cc_final: 0.7308 (p0)
REVERT: A  113 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7756 (mmtt)
REVERT: A  190 ARG cc_start: 0.8593 (mtt90) cc_final: 0.8339 (mtm180)
  outliers start: 3
  outliers final: 1
  residues processed: 39
  average time/residue: 0.3584
  time to fit residues: 14.3421
Evaluate side-chains
  38 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  113 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 13 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 6 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.150499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.120604 restraints weight = 2203.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.02
r_work: 0.3207 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   2074  Z= 0.219
  Angle     :  0.699   9.418   2840  Z= 0.354
  Chirality :  0.047   0.164    348
  Planarity :  0.004   0.026    342
  Dihedral  :  5.298  34.516    449
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.42 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  9.68 %
    Favored  : 88.17 %
  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:  0.50 (0.55), residues: 234
  helix:  2.23 (1.65), residues: 11
  sheet:  1.59 (0.52), residues: 104
  loop : -1.09 (0.54), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 273 
 TYR   0.024   0.002   TYR A 170 
 PHE   0.014   0.002   PHE A 127 
 TRP   0.005   0.001   TRP A 104 
 HIS   0.004   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 2062)
  covalent geometry    : angle       0.66198 ( 2807)
  SS BOND              : bond        0.00840 (    3)
  SS BOND              : angle       3.88100 (    6)
  hydrogen bonds       : bond        0.03005 (   79)
  hydrogen bonds       : angle       7.19932 (  234)
  link_BETA1-4         : bond        0.00406 (    3)
  link_BETA1-4         : angle       1.28747 (    9)
  link_NAG-ASN         : bond        0.00280 (    6)
  link_NAG-ASN         : angle       1.69224 (   18)

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

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

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.044 
Fit side-chains
REVERT: A   17 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.5064 (ptt)
REVERT: A  111 ASP cc_start: 0.7689 (p0) cc_final: 0.7422 (p0)
REVERT: A  113 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7635 (mttm)
REVERT: A  190 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8323 (mtm180)
  outliers start: 4
  outliers final: 1
  residues processed: 37
  average time/residue: 0.3617
  time to fit residues: 13.6498
Evaluate side-chains
  36 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  113 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 16 optimal weight:    0.2980
   chunk 20 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    0.1980
   chunk 1 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 23 optimal weight:    0.1980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.150842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.121286 restraints weight = 2219.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.00
r_work: 0.3212 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   2074  Z= 0.158
  Angle     :  0.702  14.259   2840  Z= 0.351
  Chirality :  0.046   0.160    348
  Planarity :  0.004   0.026    342
  Dihedral  :  5.047  35.040    449
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  2.99 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.90 %
    Favored  : 84.95 %
  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:  0.51 (0.56), residues: 234
  helix:  2.72 (1.65), residues: 11
  sheet:  1.54 (0.52), residues: 104
  loop : -1.09 (0.55), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 246 
 TYR   0.011   0.001   TYR A 265 
 PHE   0.015   0.002   PHE A 127 
 TRP   0.003   0.001   TRP A 104 
 HIS   0.002   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 2062)
  covalent geometry    : angle       0.64997 ( 2807)
  SS BOND              : bond        0.01090 (    3)
  SS BOND              : angle       4.65239 (    6)
  hydrogen bonds       : bond        0.02636 (   79)
  hydrogen bonds       : angle       6.91800 (  234)
  link_BETA1-4         : bond        0.00449 (    3)
  link_BETA1-4         : angle       1.34363 (    9)
  link_NAG-ASN         : bond        0.00194 (    6)
  link_NAG-ASN         : angle       1.93846 (   18)

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

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

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A   17 MET cc_start: 0.6824 (mmt) cc_final: 0.5057 (ptt)
REVERT: A  111 ASP cc_start: 0.7695 (p0) cc_final: 0.7442 (p0)
REVERT: A  113 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7632 (mttm)
REVERT: A  190 ARG cc_start: 0.8531 (mtt90) cc_final: 0.8259 (mtm180)
  outliers start: 4
  outliers final: 1
  residues processed: 36
  average time/residue: 0.4516
  time to fit residues: 16.6166
Evaluate side-chains
  33 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  113 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    0.1980
   chunk 11 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 4 optimal weight:    0.3980
   chunk 21 optimal weight:    0.4980
   chunk 7 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 14 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.151809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.122704 restraints weight = 2183.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.95
r_work: 0.3213 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   2074  Z= 0.171
  Angle     :  0.729  16.828   2840  Z= 0.361
  Chirality :  0.048   0.247    348
  Planarity :  0.004   0.025    342
  Dihedral  :  5.031  35.688    449
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.52 %
    Favored  : 83.87 %
  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:  0.37 (0.56), residues: 234
  helix:  2.69 (1.64), residues: 11
  sheet:  1.37 (0.51), residues: 105
  loop : -1.13 (0.55), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 246 
 TYR   0.025   0.002   TYR A 170 
 PHE   0.015   0.002   PHE A 127 
 TRP   0.004   0.001   TRP A 104 
 HIS   0.002   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 2062)
  covalent geometry    : angle       0.69021 ( 2807)
  SS BOND              : bond        0.01095 (    3)
  SS BOND              : angle       3.32669 (    6)
  hydrogen bonds       : bond        0.02744 (   79)
  hydrogen bonds       : angle       6.84671 (  234)
  link_BETA1-4         : bond        0.00450 (    3)
  link_BETA1-4         : angle       1.30711 (    9)
  link_NAG-ASN         : bond        0.00209 (    6)
  link_NAG-ASN         : angle       2.23430 (   18)

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

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

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A   17 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.5020 (ptt)
REVERT: A  111 ASP cc_start: 0.7763 (p0) cc_final: 0.7514 (p0)
REVERT: A  113 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7585 (mttm)
REVERT: A  190 ARG cc_start: 0.8570 (mtt90) cc_final: 0.8300 (mtm180)
  outliers start: 3
  outliers final: 1
  residues processed: 35
  average time/residue: 0.4988
  time to fit residues: 17.8365
Evaluate side-chains
  36 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  113 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 22 optimal weight:    0.0070
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0570
   overall best weight:    0.3716

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.156004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.128163 restraints weight = 2139.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.87
r_work: 0.3231 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   2074  Z= 0.164
  Angle     :  0.705  15.087   2840  Z= 0.346
  Chirality :  0.048   0.211    348
  Planarity :  0.004   0.024    342
  Dihedral  :  5.182  39.368    449
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.05 %
    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:  0.31 (0.53), residues: 234
  helix:  2.72 (1.64), residues: 11
  sheet:  1.66 (0.49), residues: 95
  loop : -1.28 (0.52), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.011   0.001   TYR A 265 
 PHE   0.015   0.002   PHE A 127 
 TRP   0.003   0.001   TRP A 104 
 HIS   0.002   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 2062)
  covalent geometry    : angle       0.65460 ( 2807)
  SS BOND              : bond        0.00907 (    3)
  SS BOND              : angle       2.89830 (    6)
  hydrogen bonds       : bond        0.02687 (   79)
  hydrogen bonds       : angle       6.65610 (  234)
  link_BETA1-4         : bond        0.00481 (    3)
  link_BETA1-4         : angle       1.24072 (    9)
  link_NAG-ASN         : bond        0.00198 (    6)
  link_NAG-ASN         : angle       2.83230 (   18)

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

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

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.046 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6476 (mmp)
REVERT: A  111 ASP cc_start: 0.7779 (p0) cc_final: 0.7536 (p0)
REVERT: A  190 ARG cc_start: 0.8523 (mtt90) cc_final: 0.8275 (mtm180)
  outliers start: 3
  outliers final: 1
  residues processed: 36
  average time/residue: 0.5200
  time to fit residues: 19.0520
Evaluate side-chains
  37 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue  108 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 6 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.150774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.121634 restraints weight = 2184.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.95
r_work: 0.3243 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   2074  Z= 0.233
  Angle     :  0.749  15.116   2840  Z= 0.369
  Chirality :  0.049   0.205    348
  Planarity :  0.004   0.025    342
  Dihedral  :  5.450  38.010    449
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.98 %
    Favored  : 84.41 %
  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:  0.20 (0.53), residues: 234
  helix:  2.42 (1.64), residues: 11
  sheet:  1.53 (0.49), residues: 95
  loop : -1.27 (0.51), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 273 
 TYR   0.014   0.002   TYR A 170 
 PHE   0.017   0.003   PHE A 127 
 TRP   0.006   0.002   TRP A 104 
 HIS   0.003   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 ( 2062)
  covalent geometry    : angle       0.71287 ( 2807)
  SS BOND              : bond        0.01091 (    3)
  SS BOND              : angle       2.65257 (    6)
  hydrogen bonds       : bond        0.03017 (   79)
  hydrogen bonds       : angle       6.88682 (  234)
  link_BETA1-4         : bond        0.00545 (    3)
  link_BETA1-4         : angle       1.32742 (    9)
  link_NAG-ASN         : bond        0.00229 (    6)
  link_NAG-ASN         : angle       2.43824 (   18)

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

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

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6558 (mmp)
REVERT: A  190 ARG cc_start: 0.8586 (mtt90) cc_final: 0.8331 (mtm180)
  outliers start: 3
  outliers final: 1
  residues processed: 37
  average time/residue: 0.5021
  time to fit residues: 18.9863
Evaluate side-chains
  37 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue  108 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.149919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.120879 restraints weight = 2136.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.94
r_work: 0.3181 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   2074  Z= 0.241
  Angle     :  0.799  17.387   2840  Z= 0.395
  Chirality :  0.050   0.239    348
  Planarity :  0.004   0.025    342
  Dihedral  :  5.514  37.599    449
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 16.67 %
    Favored  : 82.26 %
  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:  0.03 (0.52), residues: 234
  helix:  2.24 (1.65), residues: 11
  sheet:  1.07 (0.48), residues: 101
  loop : -1.17 (0.52), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 273 
 TYR   0.012   0.002   TYR A 279 
 PHE   0.016   0.003   PHE A 127 
 TRP   0.006   0.002   TRP A 104 
 HIS   0.003   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 ( 2062)
  covalent geometry    : angle       0.76012 ( 2807)
  SS BOND              : bond        0.01235 (    3)
  SS BOND              : angle       3.68482 (    6)
  hydrogen bonds       : bond        0.03095 (   79)
  hydrogen bonds       : angle       6.90656 (  234)
  link_BETA1-4         : bond        0.00490 (    3)
  link_BETA1-4         : angle       1.33594 (    9)
  link_NAG-ASN         : bond        0.00188 (    6)
  link_NAG-ASN         : angle       2.30802 (   18)

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

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

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.050 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ASP cc_start: 0.7486 (p0) cc_final: 0.7264 (p0)
REVERT: A  190 ARG cc_start: 0.8568 (mtt90) cc_final: 0.8340 (mtm180)
  outliers start: 2
  outliers final: 1
  residues processed: 34
  average time/residue: 0.4975
  time to fit residues: 17.2473
Evaluate side-chains
  34 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 33
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0970
   chunk 10 optimal weight:    0.5980
   chunk 17 optimal weight:    0.1980
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0980
   overall best weight:    0.1978

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.153749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.124105 restraints weight = 2181.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.00
r_work: 0.3210 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2074  Z= 0.119
  Angle     :  0.678  14.930   2840  Z= 0.340
  Chirality :  0.046   0.205    348
  Planarity :  0.004   0.024    342
  Dihedral  :  4.963  38.877    449
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 18.28 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.53), residues: 234
  helix:  2.68 (1.62), residues: 11
  sheet:  1.08 (0.48), residues: 101
  loop : -1.09 (0.53), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.015   0.001   TYR A 170 
 PHE   0.016   0.002   PHE A 127 
 TRP   0.001   0.000   TRP A 104 
 HIS   0.002   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 2062)
  covalent geometry    : angle       0.63944 ( 2807)
  SS BOND              : bond        0.00726 (    3)
  SS BOND              : angle       3.11802 (    6)
  hydrogen bonds       : bond        0.02642 (   79)
  hydrogen bonds       : angle       6.43973 (  234)
  link_BETA1-4         : bond        0.00510 (    3)
  link_BETA1-4         : angle       1.20740 (    9)
  link_NAG-ASN         : bond        0.00171 (    6)
  link_NAG-ASN         : angle       2.18504 (   18)

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

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

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  468 Ramachandran restraints generated.
    234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.067 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ASP cc_start: 0.7311 (p0) cc_final: 0.7099 (p0)
REVERT: A  190 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8259 (mtm180)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.4219
  time to fit residues: 15.0484
Evaluate side-chains
  35 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0870
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    0.1980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.2758

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.157033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.128834 restraints weight = 2152.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.90
r_work: 0.3220 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2074  Z= 0.135
  Angle     :  0.678  14.623   2840  Z= 0.340
  Chirality :  0.047   0.197    348
  Planarity :  0.004   0.024    342
  Dihedral  :  4.947  37.569    449
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.20 %
    Favored  : 82.80 %
  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:  0.15 (0.53), residues: 234
  helix:  2.72 (1.63), residues: 11
  sheet:  1.38 (0.48), residues: 95
  loop : -1.24 (0.52), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 273 
 TYR   0.010   0.001   TYR A 265 
 PHE   0.017   0.002   PHE A 127 
 TRP   0.003   0.001   TRP A 104 
 HIS   0.002   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 2062)
  covalent geometry    : angle       0.64346 ( 2807)
  SS BOND              : bond        0.00726 (    3)
  SS BOND              : angle       2.96082 (    6)
  hydrogen bonds       : bond        0.02708 (   79)
  hydrogen bonds       : angle       6.39453 (  234)
  link_BETA1-4         : bond        0.00509 (    3)
  link_BETA1-4         : angle       1.20318 (    9)
  link_NAG-ASN         : bond        0.00182 (    6)
  link_NAG-ASN         : angle       2.08637 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 988.87 seconds
wall clock time: 17 minutes 31.01 seconds (1051.01 seconds total)