Starting phenix.real_space_refine
on Thu Mar  6 03:16:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cx9_45982/03_2025/9cx9_45982.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cx9_45982/03_2025/9cx9_45982.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cx9_45982/03_2025/9cx9_45982.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cx9_45982/03_2025/9cx9_45982.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cx9_45982/03_2025/9cx9_45982.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cx9_45982/03_2025/9cx9_45982.cif"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.034
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
     P       6      5.49       5
     S      11      5.16       5
     C    2930      2.51       5
     N     789      2.21       5
     O     895      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4631
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 901
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 2, 'TRANS': 113}
    Chain: "L"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 805
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "V"
      Number of atoms: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 98
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "A"
      Number of atoms: 2550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 321, 2550
          Classifications: {'peptide': 321}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 295}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 277
          Classifications: {'peptide': 55}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 173
          Unresolved non-hydrogen angles: 230
          Unresolved non-hydrogen dihedrals: 148
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP%COO:plan': 1}
          Unresolved non-hydrogen planarities: 109
  Time building chain proxies: 3.62, per 1000 atoms: 0.78
  Number of scatterers: 4631
  At special positions: 0
  Unit cell: (62.208, 116.122, 116.122, 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)
     S      11     16.00
     P       6     15.00
     O     895      8.00
     N     789      7.00
     C    2930      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  92 " - pdb=" SG  CYS B  95 " 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: 1.15
  Conformation dependent library (CDL) restraints added in 602.1 milliseconds
  

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1144

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 13 sheets defined
      3.4% alpha, 39.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'H' and resid 89 through 93
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 159 through 161
      No H-bonds generated for 'chain 'A' and resid 159 through 161'
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 4.033A  pdb=" N   ASN A 281 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 9
    Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 62
      removed outlier: 4.227A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   ARG H 103 " --> pdb=" O   LEU H 110 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   LEU H 110 " --> pdb=" O   ARG H 103 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 61 through 62
      removed outlier: 4.227A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13
      removed outlier: 7.227A  pdb=" N   SER L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 46 through 47
      removed outlier: 3.581A  pdb=" N   GLN L  91 " --> pdb=" O   THR L  98 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 49 through 51
    Processing sheet with id=AA8, first strand: chain 'V' and resid 361 through 364
      removed outlier: 3.537A  pdb=" N   LYS A  10 " --> pdb=" O   ALA V 361 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 26 through 28
      removed outlier: 7.052A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 9.622A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   VAL A  53 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   GLN A  85 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   VAL A  55 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ASN A  83 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LEU A  57 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   VAL A  59 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A  79 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 127 through 129
    Processing sheet with id=AB2, first strand: chain 'A' and resid 183 through 186
    Processing sheet with id=AB3, first strand: chain 'A' and resid 207 through 208
      removed outlier: 4.004A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   LEU A 351 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 8.971A  pdb=" N   VAL A 319 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LYS A 230 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   ILE A 231 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   GLU A 257 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   ILE A 233 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL A 235 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 118 through 122

    158 hydrogen bonds defined for protein.
    411 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.23

  Time building geometry restraints manager: 1.38 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: 835
        1.33 -     1.45: 1179
        1.45 -     1.57: 2680
        1.57 -     1.69: 16
        1.69 -     1.81: 17
  Bond restraints: 4727
  Sorted by residual:
  bond pdb=" N   GLU A 110 "
       pdb=" CA  GLU A 110 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.58e+00
  bond pdb=" C   PRO A 264 "
       pdb=" O   PRO A 264 "
    ideal  model  delta    sigma   weight residual
    1.235  1.206  0.029 1.30e-02 5.92e+03 5.14e+00
  bond pdb=" C   TYR A 272 "
       pdb=" N   THR A 273 "
    ideal  model  delta    sigma   weight residual
    1.331  1.303  0.029 1.30e-02 5.92e+03 4.81e+00
  bond pdb=" N   SER A 266 "
       pdb=" CA  SER A 266 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.40e-02 5.10e+03 4.80e+00
  bond pdb=" N   ALA A 263 "
       pdb=" CA  ALA A 263 "
    ideal  model  delta    sigma   weight residual
    1.451  1.484 -0.033 1.60e-02 3.91e+03 4.36e+00
  ... (remaining 4722 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 6209
        1.60 -     3.19: 189
        3.19 -     4.79: 26
        4.79 -     6.38: 8
        6.38 -     7.98: 3
  Bond angle restraints: 6435
  Sorted by residual:
  angle pdb=" C   TYR A 272 "
        pdb=" N   THR A 273 "
        pdb=" CA  THR A 273 "
      ideal   model   delta    sigma   weight residual
     121.89  115.05    6.84 1.74e+00 3.30e-01 1.54e+01
  angle pdb=" C   TYR L  94 "
        pdb=" N   VAL L  95 "
        pdb=" CA  VAL L  95 "
      ideal   model   delta    sigma   weight residual
     120.24  122.51   -2.27 6.30e-01 2.52e+00 1.30e+01
  angle pdb=" CA  PHE A 268 "
        pdb=" C   PHE A 268 "
        pdb=" N   SER A 269 "
      ideal   model   delta    sigma   weight residual
     116.37  120.57   -4.20 1.19e+00 7.06e-01 1.25e+01
  angle pdb=" C   VAL A 271 "
        pdb=" N   TYR A 272 "
        pdb=" CA  TYR A 272 "
      ideal   model   delta    sigma   weight residual
     123.32  129.53   -6.21 1.88e+00 2.83e-01 1.09e+01
  angle pdb=" N   ALA A 258 "
        pdb=" CA  ALA A 258 "
        pdb=" C   ALA A 258 "
      ideal   model   delta    sigma   weight residual
     113.72  109.49    4.23 1.30e+00 5.92e-01 1.06e+01
  ... (remaining 6430 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 2552
       16.82 -    33.65: 210
       33.65 -    50.47: 67
       50.47 -    67.29: 12
       67.29 -    84.12: 8
  Dihedral angle restraints: 2849
    sinusoidal: 1074
      harmonic: 1775
  Sorted by residual:
  dihedral pdb=" CB  CYS L  24 "
           pdb=" SG  CYS L  24 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   56.47   36.53     1      1.00e+01 1.00e-02 1.89e+01
  dihedral pdb=" CA  SER A 269 "
           pdb=" C   SER A 269 "
           pdb=" N   LYS A 270 "
           pdb=" CA  LYS A 270 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.43  -18.57     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CB  CYS A  92 "
           pdb=" SG  CYS A  92 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -113.64   27.64     1      1.00e+01 1.00e-02 1.10e+01
  ... (remaining 2846 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 432
       0.028 -    0.055: 183
       0.055 -    0.083: 53
       0.083 -    0.110: 42
       0.110 -    0.138: 25
  Chirality restraints: 735
  Sorted by residual:
  chirality pdb=" CA  LEU A 108 "
            pdb=" N   LEU A 108 "
            pdb=" C   LEU A 108 "
            pdb=" CB  LEU A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  ILE A 119 "
            pdb=" N   ILE A 119 "
            pdb=" C   ILE A 119 "
            pdb=" CB  ILE A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  VAL B 137 "
            pdb=" N   VAL B 137 "
            pdb=" C   VAL B 137 "
            pdb=" CB  VAL B 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.51e-01
  ... (remaining 732 not shown)

  Planarity restraints: 818
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 272 "   -0.100 2.00e-02 2.50e+03   5.18e-02 5.36e+01
        pdb=" CG  TYR A 272 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 272 "    0.050 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 272 "    0.048 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 272 "    0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 272 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 272 "   -0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR A 272 "   -0.064 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 272 "   -0.026 2.00e-02 2.50e+03   5.51e-02 3.03e+01
        pdb=" C   TYR A 272 "    0.095 2.00e-02 2.50e+03
        pdb=" O   TYR A 272 "   -0.037 2.00e-02 2.50e+03
        pdb=" N   THR A 273 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN L  80 "    0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO L  81 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO L  81 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO L  81 "    0.018 5.00e-02 4.00e+02
  ... (remaining 815 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1277
        2.81 -     3.33: 3756
        3.33 -     3.85: 6987
        3.85 -     4.38: 7851
        4.38 -     4.90: 14445
  Nonbonded interactions: 34316
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU L  82 "
            pdb=" OD1 ASP L  83 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" NH2 ARG A  62 "
            pdb=" OD2 ASP A 143 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" O   ALA A 301 "
            pdb=" OH  TYR A 321 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" NE2 GLN A 130 "
            pdb=" O   LYS A 284 "
     model   vdw
     2.363 3.120
  nonbonded pdb=" OG1 THR A  98 "
            pdb=" OE1 GLU A 102 "
     model   vdw
     2.381 3.040
  ... (remaining 34311 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.370
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
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      :  0.003   0.033   4727  Z= 0.209
  Angle     :  0.668   7.978   6435  Z= 0.380
  Chirality :  0.044   0.138    735
  Planarity :  0.004   0.055    818
  Dihedral  : 14.875  84.117   1696
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 19.92 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.36), residues: 582
  helix: -0.54 (1.54), residues: 13
  sheet:  0.08 (0.34), residues: 250
  loop : -1.04 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 106 
 HIS   0.003   0.001   HIS A 159 
 PHE   0.013   0.001   PHE A 268 
 TYR   0.100   0.002   TYR A 272 
 ARG   0.010   0.001   ARG L  19 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.567 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.6766 (m-30) cc_final: 0.6323 (p0)
REVERT: A  130 GLN cc_start: 0.7953 (tt0) cc_final: 0.7605 (tt0)
  outliers start: 1
  outliers final: 1
  residues processed: 73
  average time/residue: 0.1965
  time to fit residues: 17.9530
Evaluate side-chains
  68 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   72 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  42 GLN
L   4 GLN
A 172 GLN
A 280 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.161069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.140211 restraints weight = 7052.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 1.87
r_work: 0.3700 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3579 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   4727  Z= 0.362
  Angle     :  0.659   5.991   6435  Z= 0.350
  Chirality :  0.048   0.166    735
  Planarity :  0.005   0.035    818
  Dihedral  :  5.688  37.009    674
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 16.56 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.34), residues: 582
  helix: -1.53 (1.30), residues: 15
  sheet: -0.00 (0.33), residues: 232
  loop : -1.19 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  50 
 HIS   0.006   0.001   HIS A 210 
 PHE   0.020   0.002   PHE H 105 
 TYR   0.029   0.002   TYR A 272 
 ARG   0.008   0.001   ARG L  19 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A   77 LYS cc_start: 0.7808 (tptt) cc_final: 0.7571 (tptt)
  outliers start: 26
  outliers final: 20
  residues processed: 80
  average time/residue: 0.1841
  time to fit residues: 18.5174
Evaluate side-chains
  84 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain L residue    4 GLN
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   61 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  106 GLU
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 14 optimal weight:    0.2980
   chunk 10 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 30 optimal weight:    0.3980
   chunk 31 optimal weight:    0.4980
   chunk 6 optimal weight:    0.2980
   chunk 56 optimal weight:    9.9990
   chunk 7 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
A 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.163053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.143970 restraints weight = 7085.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 2.18
r_work: 0.3692 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3569 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4727  Z= 0.215
  Angle     :  0.578   6.263   6435  Z= 0.302
  Chirality :  0.045   0.140    735
  Planarity :  0.004   0.033    818
  Dihedral  :  5.517  38.105    674
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 20.34 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.34), residues: 582
  helix: -0.36 (1.52), residues: 13
  sheet:  0.08 (0.33), residues: 232
  loop : -1.18 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.013   0.002   PHE H 105 
 TYR   0.017   0.001   TYR A 272 
 ARG   0.004   0.000   ARG L  19 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A   77 LYS cc_start: 0.7927 (tptt) cc_final: 0.7626 (tptt)
  outliers start: 23
  outliers final: 19
  residues processed: 81
  average time/residue: 0.1910
  time to fit residues: 19.4060
Evaluate side-chains
  83 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   61 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  106 GLU
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 46 optimal weight:    0.2980
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 111 HIS
A 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.160595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.141268 restraints weight = 7093.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 2.17
r_work: 0.3673 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   4727  Z= 0.314
  Angle     :  0.626   6.527   6435  Z= 0.329
  Chirality :  0.046   0.156    735
  Planarity :  0.004   0.034    818
  Dihedral  :  5.803  37.006    674
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 19.71 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.34), residues: 582
  helix: -0.61 (1.44), residues: 13
  sheet: -0.01 (0.33), residues: 231
  loop : -1.29 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  50 
 HIS   0.005   0.001   HIS A 210 
 PHE   0.019   0.002   PHE H 105 
 TYR   0.023   0.002   TYR A 272 
 ARG   0.005   0.001   ARG L  19 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 68
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A   77 LYS cc_start: 0.7958 (tptt) cc_final: 0.7545 (tptt)
REVERT: A  130 GLN cc_start: 0.8336 (tt0) cc_final: 0.7988 (tt0)
  outliers start: 32
  outliers final: 23
  residues processed: 89
  average time/residue: 0.1729
  time to fit residues: 19.4077
Evaluate side-chains
  90 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   61 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   83 ASP
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 34 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 15 optimal weight:    0.4980
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.160617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.140105 restraints weight = 7162.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 1.87
r_work: 0.3693 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4727  Z= 0.307
  Angle     :  0.635   6.113   6435  Z= 0.331
  Chirality :  0.046   0.142    735
  Planarity :  0.004   0.034    818
  Dihedral  :  5.887  38.575    674
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 20.34 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.34), residues: 582
  helix: -0.88 (1.32), residues: 13
  sheet: -0.11 (0.33), residues: 231
  loop : -1.32 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  50 
 HIS   0.005   0.001   HIS A 210 
 PHE   0.018   0.002   PHE H 105 
 TYR   0.022   0.002   TYR A 272 
 ARG   0.005   0.000   ARG A 177 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 66
  time to evaluate  : 0.546 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7785 (mm) cc_final: 0.7491 (mt)
REVERT: A   77 LYS cc_start: 0.7851 (tptt) cc_final: 0.7487 (tptt)
REVERT: A  130 GLN cc_start: 0.8239 (tt0) cc_final: 0.8017 (tt0)
  outliers start: 31
  outliers final: 29
  residues processed: 85
  average time/residue: 0.1798
  time to fit residues: 19.3542
Evaluate side-chains
  92 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   61 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   83 ASP
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
L   4 GLN
A 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.159749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.139307 restraints weight = 7097.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 1.88
r_work: 0.3684 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3563 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4727  Z= 0.307
  Angle     :  0.637   5.875   6435  Z= 0.332
  Chirality :  0.046   0.142    735
  Planarity :  0.004   0.035    818
  Dihedral  :  5.953  39.930    674
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  7.34 %
    Allowed  : 20.34 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.33), residues: 582
  helix: -1.16 (1.27), residues: 13
  sheet: -0.15 (0.32), residues: 231
  loop : -1.36 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  50 
 HIS   0.005   0.001   HIS A 210 
 PHE   0.018   0.002   PHE H 105 
 TYR   0.020   0.002   TYR A 272 
 ARG   0.007   0.001   ARG L  19 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 66
  time to evaluate  : 0.559 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7840 (mm) cc_final: 0.7594 (mt)
REVERT: A   77 LYS cc_start: 0.7762 (tptt) cc_final: 0.7382 (tptt)
REVERT: A  130 GLN cc_start: 0.8238 (tt0) cc_final: 0.8003 (tt0)
  outliers start: 35
  outliers final: 34
  residues processed: 90
  average time/residue: 0.1767
  time to fit residues: 20.1353
Evaluate side-chains
  98 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 64
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   60 TYR
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   61 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   83 ASP
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0770
   chunk 52 optimal weight:    0.3980
   chunk 20 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.161534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.141570 restraints weight = 7035.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 1.81
r_work: 0.3710 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3588 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4727  Z= 0.222
  Angle     :  0.597   8.249   6435  Z= 0.307
  Chirality :  0.045   0.142    735
  Planarity :  0.004   0.034    818
  Dihedral  :  5.743  37.972    674
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 22.22 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.34), residues: 582
  helix: -1.14 (1.30), residues: 13
  sheet:  0.00 (0.33), residues: 231
  loop : -1.24 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  50 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.014   0.002   PHE A  27 
 TYR   0.015   0.001   TYR A 272 
 ARG   0.006   0.000   ARG L  19 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 65
  time to evaluate  : 0.523 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7739 (mm) cc_final: 0.7466 (mt)
REVERT: A   77 LYS cc_start: 0.7731 (tptt) cc_final: 0.7372 (tptt)
REVERT: A  130 GLN cc_start: 0.8235 (tt0) cc_final: 0.8000 (tt0)
REVERT: A  165 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7932 (ptp-110)
  outliers start: 31
  outliers final: 27
  residues processed: 84
  average time/residue: 0.1991
  time to fit residues: 20.8716
Evaluate side-chains
  90 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 62
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   61 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   83 ASP
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  106 GLU
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 41 optimal weight:    0.3980
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 32 optimal weight:    0.1980
   chunk 58 optimal weight:    0.0670
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
L   4 GLN
A 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.162067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.142092 restraints weight = 7043.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 1.81
r_work: 0.3717 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4727  Z= 0.205
  Angle     :  0.582   6.135   6435  Z= 0.299
  Chirality :  0.044   0.147    735
  Planarity :  0.004   0.036    818
  Dihedral  :  5.596  38.468    674
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 22.22 %
    Favored  : 70.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.34), residues: 582
  helix: -1.27 (1.29), residues: 13
  sheet:  0.11 (0.33), residues: 231
  loop : -1.14 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 106 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.013   0.002   PHE A  27 
 TYR   0.014   0.001   TYR A 272 
 ARG   0.007   0.000   ARG L  19 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 67
  time to evaluate  : 0.522 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7728 (mm) cc_final: 0.7462 (mt)
REVERT: A   77 LYS cc_start: 0.7693 (tptt) cc_final: 0.7378 (tptt)
REVERT: A  130 GLN cc_start: 0.8234 (tt0) cc_final: 0.8012 (tt0)
REVERT: A  165 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7882 (ptp-110)
REVERT: A  320 SER cc_start: 0.8202 (p) cc_final: 0.7921 (t)
  outliers start: 33
  outliers final: 28
  residues processed: 84
  average time/residue: 0.1878
  time to fit residues: 19.6321
Evaluate side-chains
  97 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 68
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   61 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   83 ASP
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  106 GLU
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  165 ARG
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 50 optimal weight:    0.4980
   chunk 9 optimal weight:    0.0980
   chunk 54 optimal weight:    0.0020
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 42 optimal weight:    0.1980
   chunk 30 optimal weight:    0.0470
   overall best weight:    0.1686

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.165220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.145335 restraints weight = 7051.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 1.84
r_work: 0.3760 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4727  Z= 0.144
  Angle     :  0.564  11.578   6435  Z= 0.284
  Chirality :  0.043   0.141    735
  Planarity :  0.004   0.034    818
  Dihedral  :  5.259  39.941    674
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 23.48 %
    Favored  : 70.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.35), residues: 582
  helix: -1.04 (1.37), residues: 13
  sheet:  0.34 (0.34), residues: 232
  loop : -1.03 (0.35), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 106 
 HIS   0.003   0.001   HIS A 210 
 PHE   0.012   0.001   PHE A  27 
 TYR   0.009   0.001   TYR A 272 
 ARG   0.009   0.001   ARG L  19 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.492 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7584 (mm) cc_final: 0.7354 (mt)
REVERT: A   18 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8191 (pt)
REVERT: A   77 LYS cc_start: 0.7788 (tptt) cc_final: 0.7500 (tptt)
REVERT: A  320 SER cc_start: 0.8186 (p) cc_final: 0.7964 (t)
  outliers start: 27
  outliers final: 23
  residues processed: 87
  average time/residue: 0.1704
  time to fit residues: 18.7533
Evaluate side-chains
  94 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain L residue  106 GLU
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 20 optimal weight:    0.0980
   chunk 31 optimal weight:    0.1980
   chunk 34 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 10 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0970
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.1778

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

Flipped N/Q/H residues before XYZ refinement:
L   4 GLN
A 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.165926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.147474 restraints weight = 7125.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 2.21
r_work: 0.3750 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3625 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4727  Z= 0.147
  Angle     :  0.559  10.764   6435  Z= 0.281
  Chirality :  0.043   0.137    735
  Planarity :  0.004   0.038    818
  Dihedral  :  5.069  41.130    674
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 23.06 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.35), residues: 582
  helix: -1.61 (1.30), residues: 15
  sheet:  0.54 (0.34), residues: 226
  loop : -0.97 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 106 
 HIS   0.003   0.001   HIS A 210 
 PHE   0.010   0.001   PHE A  27 
 TYR   0.017   0.001   TYR A 113 
 ARG   0.008   0.001   ARG L  19 

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.552 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7533 (mm) cc_final: 0.7321 (mt)
REVERT: A   18 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8177 (pt)
REVERT: A   77 LYS cc_start: 0.7828 (tptt) cc_final: 0.7545 (tptt)
REVERT: A  320 SER cc_start: 0.8135 (p) cc_final: 0.7933 (t)
  outliers start: 25
  outliers final: 23
  residues processed: 85
  average time/residue: 0.2085
  time to fit residues: 21.9421
Evaluate side-chains
  94 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   86 THR
Chi-restraints excluded: chain L residue  106 GLU
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  328 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 4 optimal weight:    0.0000
   chunk 56 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 0 optimal weight:    0.1980
   chunk 41 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0060
   chunk 46 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.3200

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.164458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.145921 restraints weight = 7151.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 2.20
r_work: 0.3723 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3598 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4727  Z= 0.183
  Angle     :  0.573  10.321   6435  Z= 0.289
  Chirality :  0.044   0.137    735
  Planarity :  0.004   0.037    818
  Dihedral  :  5.148  40.601    674
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 23.48 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.35), residues: 582
  helix: -1.74 (1.25), residues: 15
  sheet:  0.50 (0.34), residues: 232
  loop : -0.93 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 106 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.011   0.001   PHE A  27 
 TYR   0.012   0.001   TYR A 272 
 ARG   0.009   0.001   ARG L  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2932.30 seconds
wall clock time: 51 minutes 8.37 seconds (3068.37 seconds total)