Starting phenix.real_space_refine
on Tue Jan 14 00:10:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cx9_45982/01_2025/9cx9_45982.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cx9_45982/01_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_45982/01_2025/9cx9_45982.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cx9_45982/01_2025/9cx9_45982.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cx9_45982/01_2025/9cx9_45982.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cx9_45982/01_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 3.59, 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: 1.10
  Conformation dependent library (CDL) restraints added in 515.3 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: 0.61
  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: 1.21

  Time building geometry restraints manager: 1.28 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:             1.500
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     14.990
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.540
-------------------------------------------------------------------------------
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  : 0.568 
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: 0.2018
  time to fit residues: 18.3980
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  : 0.514 
-------------------------------------------------------------------------------
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 = 69)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.140250 restraints weight = 7052.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.85
r_work: 0.3698 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3577 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
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  : 0.580 
Fit side-chains
REVERT: A   77 LYS cc_start: 0.7803 (tptt) cc_final: 0.7559 (tptt)
  outliers start: 26
  outliers final: 20
  residues processed: 80
  average time/residue: 0.1852
  time to fit residues: 18.7248
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  : 0.529 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0970
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    0.1980
   chunk 56 optimal weight:    9.9990
   chunk 7 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.163341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.144180 restraints weight = 7083.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 2.20
r_work: 0.3699 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4727  Z= 0.193
  Angle     :  0.568   6.044   6435  Z= 0.297
  Chirality :  0.045   0.141    735
  Planarity :  0.004   0.034    818
  Dihedral  :  5.451  38.456    674
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 19.92 %
    Favored  : 75.26 %
  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: -0.90 (0.35), residues: 582
  helix: -0.34 (1.52), residues: 13
  sheet:  0.12 (0.33), residues: 232
  loop : -1.14 (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   0.011   0.001   PHE H 105 
 TYR   0.017   0.001   TYR A 272 
 ARG   0.006   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
  93 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A   77 LYS cc_start: 0.7919 (tptt) cc_final: 0.7614 (tptt)
  outliers start: 23
  outliers final: 18
  residues processed: 82
  average time/residue: 0.1872
  time to fit residues: 19.1959
Evaluate side-chains
  82 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
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   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:    0.1980
   chunk 10 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 12 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:
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 = 0.4062 r_free = 0.4062 target = 0.160816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.141535 restraints weight = 7109.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 2.16
r_work: 0.3659 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3535 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2142

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= 0.312
  Angle     :  0.622   6.641   6435  Z= 0.328
  Chirality :  0.046   0.155    735
  Planarity :  0.004   0.034    818
  Dihedral  :  5.753  37.312    674
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 20.13 %
    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: -1.04 (0.34), residues: 582
  helix: -0.67 (1.42), residues: 13
  sheet:  0.05 (0.33), residues: 231
  loop : -1.25 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  50 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.019   0.002   PHE H 105 
 TYR   0.023   0.002   TYR A 272 
 ARG   0.005   0.000   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: 30
    poor density    : 70
  time to evaluate  : 0.619 
Fit side-chains
REVERT: H   32 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8992 (p)
REVERT: A   77 LYS cc_start: 0.7972 (tptt) cc_final: 0.7551 (tptt)
  outliers start: 30
  outliers final: 22
  residues processed: 89
  average time/residue: 0.1827
  time to fit residues: 20.5270
Evaluate side-chains
  89 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
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   60 TYR
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   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  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:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9990
   chunk 37 optimal weight:    0.4980
   chunk 15 optimal weight:    0.6980
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4043 r_free = 0.4043 target = 0.159988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.139482 restraints weight = 7305.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 1.86
r_work: 0.3684 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4727  Z= 0.342
  Angle     :  0.663   7.368   6435  Z= 0.346
  Chirality :  0.047   0.140    735
  Planarity :  0.005   0.036    818
  Dihedral  :  5.973  39.759    674
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  7.13 %
    Allowed  : 19.29 %
    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: -1.26 (0.34), residues: 582
  helix: -1.01 (1.30), residues: 13
  sheet: -0.15 (0.33), residues: 231
  loop : -1.34 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  50 
 HIS   0.005   0.002   HIS A 210 
 PHE   0.019   0.002   PHE H 105 
 TYR   0.023   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
  101 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 67
  time to evaluate  : 0.577 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7796 (mm) cc_final: 0.7511 (mt)
REVERT: A   77 LYS cc_start: 0.7842 (tptt) cc_final: 0.7378 (tptt)
  outliers start: 34
  outliers final: 31
  residues processed: 89
  average time/residue: 0.1786
  time to fit residues: 20.1793
Evaluate side-chains
  93 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 62
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
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   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   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  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  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:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0670
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 1 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
L   4 GLN
A 130 GLN
A 172 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.160826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.141401 restraints weight = 7110.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 2.25
r_work: 0.3681 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3553 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4727  Z= 0.254
  Angle     :  0.611   6.431   6435  Z= 0.316
  Chirality :  0.045   0.145    735
  Planarity :  0.004   0.035    818
  Dihedral  :  5.785  38.625    674
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 22.64 %
    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: -1.18 (0.34), residues: 582
  helix: -1.22 (1.27), residues: 13
  sheet: -0.12 (0.33), residues: 231
  loop : -1.26 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP H  50 
 HIS   0.005   0.001   HIS A 210 
 PHE   0.014   0.002   PHE H 105 
 TYR   0.017   0.002   TYR A 272 
 ARG   0.006   0.000   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
  94 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 65
  time to evaluate  : 0.531 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7802 (mm) cc_final: 0.7494 (mt)
REVERT: A   77 LYS cc_start: 0.7786 (tptt) cc_final: 0.7391 (tptt)
  outliers start: 29
  outliers final: 27
  residues processed: 82
  average time/residue: 0.1835
  time to fit residues: 19.0755
Evaluate side-chains
  89 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 62
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
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   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   40 VAL
Chi-restraints excluded: chain A residue   53 VAL
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  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  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:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0020
   chunk 53 optimal weight:    0.4980
   chunk 51 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 40 optimal weight:    0.1980
   overall best weight:    0.4188

-------------------------------------------------------------------------------
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 = 0.4072 r_free = 0.4072 target = 0.161685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.141628 restraints weight = 7025.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 1.80
r_work: 0.3716 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3602 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4727  Z= 0.215
  Angle     :  0.596   8.016   6435  Z= 0.304
  Chirality :  0.045   0.140    735
  Planarity :  0.004   0.036    818
  Dihedral  :  5.666  38.146    674
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 23.27 %
    Favored  : 70.02 %
  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: -1.03 (0.34), residues: 582
  helix: -1.20 (1.32), residues: 13
  sheet:  0.03 (0.33), residues: 231
  loop : -1.19 (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   0.014   0.002   PHE A  27 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.007   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
  97 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 65
  time to evaluate  : 0.504 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7712 (mm) cc_final: 0.7445 (mt)
REVERT: A   77 LYS cc_start: 0.7716 (tptt) cc_final: 0.7497 (tptt)
REVERT: A  165 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7902 (ptp-110)
  outliers start: 32
  outliers final: 29
  residues processed: 83
  average time/residue: 0.1982
  time to fit residues: 20.4849
Evaluate side-chains
  92 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 62
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
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   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   18 LEU
Chi-restraints excluded: chain A residue   40 VAL
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  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=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:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 41 optimal weight:    0.1980
   chunk 16 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4058 r_free = 0.4058 target = 0.160464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.141299 restraints weight = 7049.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 2.21
r_work: 0.3682 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3553 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4727  Z= 0.274
  Angle     :  0.623   6.176   6435  Z= 0.322
  Chirality :  0.046   0.153    735
  Planarity :  0.004   0.036    818
  Dihedral  :  5.814  37.789    674
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 23.27 %
    Favored  : 69.81 %
  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: -1.42 (1.26), residues: 13
  sheet: -0.01 (0.33), residues: 231
  loop : -1.22 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP H  50 
 HIS   0.005   0.001   HIS H  38 
 PHE   0.017   0.002   PHE H 105 
 TYR   0.017   0.002   TYR A 272 
 ARG   0.007   0.001   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
  97 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 64
  time to evaluate  : 0.499 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7815 (mm) cc_final: 0.7543 (mt)
REVERT: A   77 LYS cc_start: 0.7780 (tptt) cc_final: 0.7399 (tptt)
REVERT: A  165 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7920 (ptp-110)
  outliers start: 33
  outliers final: 32
  residues processed: 84
  average time/residue: 0.1939
  time to fit residues: 20.4321
Evaluate side-chains
  95 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 62
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
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   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   40 VAL
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  108 LEU
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  207 ILE
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 9 optimal weight:    0.2980
   chunk 54 optimal weight:    0.0870
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0000
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.2962

-------------------------------------------------------------------------------
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 = 0.4081 r_free = 0.4081 target = 0.163029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.144244 restraints weight = 7178.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 2.19
r_work: 0.3704 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3577 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4727  Z= 0.177
  Angle     :  0.590  11.980   6435  Z= 0.297
  Chirality :  0.044   0.142    735
  Planarity :  0.004   0.035    818
  Dihedral  :  5.537  38.921    674
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 24.11 %
    Favored  : 70.02 %
  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: -0.85 (0.35), residues: 582
  helix: -1.31 (1.30), residues: 13
  sheet:  0.19 (0.33), residues: 232
  loop : -1.09 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 106 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.013   0.001   PHE A  27 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.008   0.000   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
  94 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 66
  time to evaluate  : 0.539 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7722 (mm) cc_final: 0.7449 (mt)
REVERT: A   77 LYS cc_start: 0.7726 (tptt) cc_final: 0.7408 (tptt)
REVERT: A  320 SER cc_start: 0.8171 (p) cc_final: 0.7792 (t)
  outliers start: 28
  outliers final: 26
  residues processed: 80
  average time/residue: 0.1942
  time to fit residues: 19.4966
Evaluate side-chains
  90 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 64
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
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  111 ASP
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   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   40 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  108 LEU
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  298 THR
Chi-restraints excluded: chain A residue  317 ILE
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:    0.4980
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 56 optimal weight:    8.9990
   chunk 10 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   chunk 44 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4069 r_free = 0.4069 target = 0.161292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.142346 restraints weight = 6994.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 2.19
r_work: 0.3693 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3563 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4727  Z= 0.238
  Angle     :  0.616  11.673   6435  Z= 0.312
  Chirality :  0.045   0.140    735
  Planarity :  0.004   0.037    818
  Dihedral  :  5.660  40.424    674
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 24.32 %
    Favored  : 70.02 %
  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: -0.87 (0.35), residues: 582
  helix: -1.30 (1.29), residues: 13
  sheet:  0.17 (0.33), residues: 231
  loop : -1.09 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.004   0.001   HIS H  38 
 PHE   0.014   0.002   PHE H 105 
 TYR   0.019   0.002   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
  92 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 65
  time to evaluate  : 0.523 
Fit side-chains
REVERT: H   89 LEU cc_start: 0.7775 (mm) cc_final: 0.7494 (mt)
REVERT: A   77 LYS cc_start: 0.7831 (tptt) cc_final: 0.7449 (tptt)
REVERT: A  320 SER cc_start: 0.8191 (p) cc_final: 0.7801 (t)
  outliers start: 27
  outliers final: 27
  residues processed: 81
  average time/residue: 0.1864
  time to fit residues: 19.0760
Evaluate side-chains
  91 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 64
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
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  111 ASP
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   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   40 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  108 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 9 optimal weight:    0.2980
   chunk 0 optimal weight:    0.3980
   chunk 41 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.4064 r_free = 0.4064 target = 0.160906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.141863 restraints weight = 7038.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 2.21
r_work: 0.3681 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3550 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4727  Z= 0.250
  Angle     :  0.618  10.927   6435  Z= 0.315
  Chirality :  0.045   0.140    735
  Planarity :  0.004   0.037    818
  Dihedral  :  5.768  42.348    674
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 23.90 %
    Favored  : 69.81 %
  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: -1.50 (1.25), residues: 13
  sheet:  0.11 (0.33), residues: 231
  loop : -1.13 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP H  50 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.015   0.002   PHE H 105 
 TYR   0.020   0.002   TYR A 113 
 ARG   0.008   0.001   ARG L  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2903.21 seconds
wall clock time: 52 minutes 4.31 seconds (3124.31 seconds total)