Starting phenix.real_space_refine
on Tue Feb 11 09:20:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mlz_23914/02_2025/7mlz_23914.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mlz_23914/02_2025/7mlz_23914.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mlz_23914/02_2025/7mlz_23914.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mlz_23914/02_2025/7mlz_23914.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mlz_23914/02_2025/7mlz_23914.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mlz_23914/02_2025/7mlz_23914.cif"
  }
  resolution = 3.71
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    3073      2.51       5
     N     809      2.21       5
     O     960      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4864
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1551
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "H"
      Number of atoms: 1611
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 215, 1611
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 202}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "L"
      Number of atoms: 1641
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 213, 1641
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200}
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 2.21, per 1000 atoms: 0.45
  Number of scatterers: 4864
  At special positions: 0
  Unit cell: (86.427, 61.983, 138.807, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O     960      8.00
     N     809      7.00
     C    3073      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  97 " - pdb=" SG  CYS H 100B" distance=2.04
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " 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
  Links applied
    ALPHA1-3
      " BMA B   3 " - " MAN B   4 "
    ALPHA1-6
      " BMA B   3 " - " MAN B   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 600.7 milliseconds
  

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1152

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 14 sheets defined
      5.0% alpha, 18.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 4.049A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 3.706A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.674A  pdb=" N   VAL A 407 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN A 409 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 73 through 77
      removed outlier: 3.968A  pdb=" N   THR H  77 " --> pdb=" O   SER H  74 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 126
      removed outlier: 3.598A  pdb=" N   LEU L 125 " --> pdb=" O   ASP L 122 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
      removed outlier: 3.689A  pdb=" N   ILE A 402 " --> pdb=" O   TYR A 508 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358
    Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 6
      removed outlier: 3.599A  pdb=" N   VAL H   5 " --> pdb=" O   LYS H  23 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.896A  pdb=" N   LYS H  12 " --> pdb=" O   THR H 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 19
    Processing sheet with id=AA6, first strand: chain 'H' and resid 33 through 38
      removed outlier: 6.146A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL H  52 " --> pdb=" O   ASN H  56 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ASN H  56 " --> pdb=" O   VAL H  52 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 93 through 94
    Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124
      removed outlier: 4.262A  pdb=" N   GLY H 139 " --> pdb=" O   LEU H 124 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   SER H 177 " --> pdb=" O   ALA H 168 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ALA H 168 " --> pdb=" O   SER H 177 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   SER H 179 " --> pdb=" O   PHE H 166 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 198 through 200
      removed outlier: 3.504A  pdb=" N   THR H 205 " --> pdb=" O   HIS H 200 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12
      removed outlier: 5.825A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'L' and resid 20 through 24
    Processing sheet with id=AB3, first strand: chain 'L' and resid 33 through 37
      removed outlier: 4.059A  pdb=" N   ALA L  34 " --> pdb=" O   GLN L  89 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   TYR L  87 " --> pdb=" O   TYR L  36 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 117 through 118
      removed outlier: 3.538A  pdb=" N   THR L 178 " --> pdb=" O   GLN L 160 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN L 160 " --> pdb=" O   THR L 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 146 through 147
      removed outlier: 3.520A  pdb=" N   GLU L 195 " --> pdb=" O   GLN L 147 " (cutoff:3.500A)

    74 hydrogen bonds defined for protein.
    171 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: 1.10

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1544
        1.35 -     1.48: 1377
        1.48 -     1.60: 2037
        1.60 -     1.73: 0
        1.73 -     1.85: 26
  Bond restraints: 4984
  Sorted by residual:
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.46e+00
  bond pdb=" C1  MAN B   4 "
       pdb=" C2  MAN B   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.569 -0.043 2.00e-02 2.50e+03 4.73e+00
  bond pdb=" C1  BMA B   3 "
       pdb=" C2  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.560 -0.041 2.00e-02 2.50e+03 4.30e+00
  bond pdb=" C1  MAN B   4 "
       pdb=" O5  MAN B   4 "
    ideal  model  delta    sigma   weight residual
    1.399  1.432 -0.033 2.00e-02 2.50e+03 2.72e+00
  bond pdb=" C   GLN A 498 "
       pdb=" N   PRO A 499 "
    ideal  model  delta    sigma   weight residual
    1.334  1.346 -0.013 8.40e-03 1.42e+04 2.34e+00
  ... (remaining 4979 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 6440
        1.62 -     3.25: 262
        3.25 -     4.87: 59
        4.87 -     6.49: 15
        6.49 -     8.12: 6
  Bond angle restraints: 6782
  Sorted by residual:
  angle pdb=" C   THR H 191 "
        pdb=" N   GLN H 192 "
        pdb=" CA  GLN H 192 "
      ideal   model   delta    sigma   weight residual
     121.54  128.49   -6.95 1.91e+00 2.74e-01 1.33e+01
  angle pdb=" CA  CYS A 379 "
        pdb=" CB  CYS A 379 "
        pdb=" SG  CYS A 379 "
      ideal   model   delta    sigma   weight residual
     114.40  122.52   -8.12 2.30e+00 1.89e-01 1.25e+01
  angle pdb=" C   PHE A 347 "
        pdb=" N   ALA A 348 "
        pdb=" CA  ALA A 348 "
      ideal   model   delta    sigma   weight residual
     121.54  128.07   -6.53 1.91e+00 2.74e-01 1.17e+01
  angle pdb=" C   SER L  30 "
        pdb=" N   SER L  31 "
        pdb=" CA  SER L  31 "
      ideal   model   delta    sigma   weight residual
     121.54  127.13   -5.59 1.91e+00 2.74e-01 8.56e+00
  angle pdb=" CA  GLY H  55 "
        pdb=" C   GLY H  55 "
        pdb=" N   ASN H  56 "
      ideal   model   delta    sigma   weight residual
     117.06  114.03    3.03 1.08e+00 8.57e-01 7.89e+00
  ... (remaining 6777 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.98: 2835
       22.98 -    45.97: 165
       45.97 -    68.95: 14
       68.95 -    91.94: 12
       91.94 -   114.92: 4
  Dihedral angle restraints: 3030
    sinusoidal: 1225
      harmonic: 1805
  Sorted by residual:
  dihedral pdb=" CB  CYS L 134 "
           pdb=" SG  CYS L 134 "
           pdb=" SG  CYS L 194 "
           pdb=" CB  CYS L 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.47  -86.47     1      1.00e+01 1.00e-02 9.01e+01
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   15.07   77.93     1      1.00e+01 1.00e-02 7.59e+01
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   32.88   60.12     1      1.00e+01 1.00e-02 4.82e+01
  ... (remaining 3027 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 568
       0.051 -    0.101: 154
       0.101 -    0.152: 35
       0.152 -    0.203: 4
       0.203 -    0.254: 2
  Chirality restraints: 763
  Sorted by residual:
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.53    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CB  ILE L  48 "
            pdb=" CA  ILE L  48 "
            pdb=" CG1 ILE L  48 "
            pdb=" CG2 ILE L  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  LYS H 201 "
            pdb=" N   LYS H 201 "
            pdb=" C   LYS H 201 "
            pdb=" CB  LYS H 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.34e-01
  ... (remaining 760 not shown)

  Planarity restraints: 868
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA L 112 "   -0.034 5.00e-02 4.00e+02   5.16e-02 4.26e+00
        pdb=" N   PRO L 113 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO L 113 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L 113 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 429 "    0.014 2.00e-02 2.50e+03   1.53e-02 4.12e+00
        pdb=" CG  PHE A 429 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 429 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 429 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 429 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 429 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 429 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 411 "   -0.031 5.00e-02 4.00e+02   4.75e-02 3.62e+00
        pdb=" N   PRO A 412 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 412 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 412 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 865 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 212
        2.70 -     3.25: 5009
        3.25 -     3.80: 7178
        3.80 -     4.35: 9034
        4.35 -     4.90: 14971
  Nonbonded interactions: 36404
  Sorted by model distance:
  nonbonded pdb=" OG1 THR H  28 "
            pdb=" O   CYS H  97 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" OG1 THR L  20 "
            pdb=" O   LEU L  73 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   THR A 393 "
            pdb=" OG1 THR A 523 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   ARG L  61 "
            pdb=" OG  SER L  76 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" NH2 ARG A 357 "
            pdb=" OH  TYR A 396 "
     model   vdw
     2.236 3.120
  ... (remaining 36399 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 group one per residue
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:             19.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     11.130
  Find NCS groups from input model:        0.070
  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:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6220
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      :  0.004   0.055   4984  Z= 0.265
  Angle     :  0.821   8.116   6782  Z= 0.421
  Chirality :  0.050   0.254    763
  Planarity :  0.005   0.052    867
  Dihedral  : 14.730 114.921   1851
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 18.13
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 17.37 %
    Favored  : 82.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  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: -4.08 (0.31), residues: 616
  helix: -4.58 (0.49), residues: 20
  sheet: -2.30 (0.39), residues: 167
  loop : -2.99 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H  47 
 HIS   0.004   0.001   HIS H 200 
 PHE   0.036   0.002   PHE A 429 
 TYR   0.029   0.002   TYR L  49 
 ARG   0.009   0.001   ARG H  38 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.8718 (mp) cc_final: 0.8491 (mm)
REVERT: H   72 ASP cc_start: 0.7392 (t0) cc_final: 0.6045 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.2196
  time to fit residues: 24.0198
Evaluate side-chains
  69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    0.3980
   chunk 47 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 138 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.093917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.085507 restraints weight = 22649.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.087322 restraints weight = 14133.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.088564 restraints weight = 9720.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3952 r_free = 0.3952    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3952 r_free = 0.3952    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   4984  Z= 0.247
  Angle     :  0.776   8.582   6782  Z= 0.396
  Chirality :  0.049   0.180    763
  Planarity :  0.006   0.050    867
  Dihedral  : 11.324  91.494    777
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 16.23 %
    Favored  : 83.60 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.15 %
    Favored  : 86.54 %
  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: -4.25 (0.30), residues: 616
  helix: -4.10 (0.49), residues: 26
  sheet: -2.32 (0.39), residues: 168
  loop : -3.16 (0.27), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP L  35 
 HIS   0.005   0.001   HIS L 189 
 PHE   0.024   0.002   PHE H  27 
 TYR   0.014   0.002   TYR H  96 
 ARG   0.008   0.001   ARG H  71 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.8831 (mp) cc_final: 0.8590 (mm)
REVERT: H   38 ARG cc_start: 0.8107 (tmm-80) cc_final: 0.7812 (tmm-80)
REVERT: H   72 ASP cc_start: 0.8321 (t0) cc_final: 0.7665 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 80
  average time/residue: 0.1957
  time to fit residues: 19.7204
Evaluate side-chains
  76 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.093706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.085281 restraints weight = 22839.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.087130 restraints weight = 14178.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.088368 restraints weight = 9679.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3954
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3954 r_free = 0.3954    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3954 r_free = 0.3954    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3954
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6485
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   4984  Z= 0.234
  Angle     :  0.762   8.812   6782  Z= 0.386
  Chirality :  0.049   0.163    763
  Planarity :  0.005   0.049    867
  Dihedral  : 10.503  81.393    777
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 16.88 %
    Favored  : 82.95 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 17.76 %
    Favored  : 81.12 %
  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: -4.36 (0.30), residues: 616
  helix: -3.95 (0.55), residues: 26
  sheet: -2.33 (0.39), residues: 167
  loop : -3.29 (0.26), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H  47 
 HIS   0.003   0.001   HIS L 189 
 PHE   0.027   0.002   PHE H  27 
 TYR   0.012   0.001   TYR A 453 
 ARG   0.008   0.001   ARG H  71 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.8829 (mp) cc_final: 0.8547 (mm)
REVERT: H   72 ASP cc_start: 0.8220 (t0) cc_final: 0.7876 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 84
  average time/residue: 0.2357
  time to fit residues: 24.3644
Evaluate side-chains
  77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 2 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.093050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.084643 restraints weight = 22975.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.086482 restraints weight = 14285.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.087731 restraints weight = 9791.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3940 r_free = 0.3940    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3940 r_free = 0.3940    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4984  Z= 0.244
  Angle     :  0.742   8.426   6782  Z= 0.380
  Chirality :  0.048   0.162    763
  Planarity :  0.005   0.048    867
  Dihedral  :  9.321  66.848    777
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 18.34 %
    Favored  : 81.49 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.50 %
    Favored  : 79.07 %
  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: -4.39 (0.29), residues: 616
  helix: -3.84 (0.59), residues: 27
  sheet: -2.35 (0.39), residues: 167
  loop : -3.31 (0.26), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H  47 
 HIS   0.003   0.001   HIS L 198 
 PHE   0.029   0.002   PHE H  27 
 TYR   0.016   0.002   TYR L 140 
 ARG   0.008   0.001   ARG H  71 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.8876 (mp) cc_final: 0.8602 (mm)
REVERT: H   72 ASP cc_start: 0.8200 (t0) cc_final: 0.7870 (t0)
REVERT: H  144 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8030 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 89
  average time/residue: 0.1884
  time to fit residues: 21.2721
Evaluate side-chains
  78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain H residue  140 CYS
Chi-restraints excluded: chain H residue  144 ASP
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.3980
   chunk 23 optimal weight:    0.0970
   chunk 18 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0570
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.093944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.085524 restraints weight = 22965.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.087340 restraints weight = 14246.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.088628 restraints weight = 9767.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3938
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3938 r_free = 0.3938    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3938 r_free = 0.3938    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4984  Z= 0.199
  Angle     :  0.744   7.848   6782  Z= 0.377
  Chirality :  0.048   0.257    763
  Planarity :  0.005   0.050    867
  Dihedral  :  8.292  59.500    777
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 14.94 %
    Favored  : 84.90 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.75 %
    Favored  : 77.01 %
  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: -4.30 (0.30), residues: 616
  helix: -3.70 (0.62), residues: 27
  sheet: -2.37 (0.39), residues: 163
  loop : -3.22 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.003   0.001   HIS L 198 
 PHE   0.032   0.002   PHE H  27 
 TYR   0.036   0.002   TYR L  49 
 ARG   0.006   0.001   ARG H  71 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.8895 (mp) cc_final: 0.8631 (mm)
REVERT: H   72 ASP cc_start: 0.8270 (t0) cc_final: 0.7812 (t0)
REVERT: H  100 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6848 (t80)
REVERT: H  117 LYS cc_start: 0.7569 (pptt) cc_final: 0.6303 (pptt)
REVERT: H  144 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.7267 (t0)
REVERT: H  201 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8575 (ptmm)
  outliers start: 12
  outliers final: 7
  residues processed: 90
  average time/residue: 0.1921
  time to fit residues: 22.0094
Evaluate side-chains
  83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain H residue  100 PHE
Chi-restraints excluded: chain H residue  144 ASP
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  181 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.090172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.081572 restraints weight = 23204.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.083494 restraints weight = 14092.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.084801 restraints weight = 9586.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3854 r_free = 0.3854    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3854 r_free = 0.3854    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.124   4984  Z= 0.400
  Angle     :  0.853   9.827   6782  Z= 0.444
  Chirality :  0.051   0.208    763
  Planarity :  0.006   0.052    867
  Dihedral  :  7.801  50.799    777
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 19.72
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 19.16 %
    Favored  : 80.68 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 20.00 %
    Favored  : 75.89 %
  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: -4.52 (0.29), residues: 616
  helix: -3.29 (0.72), residues: 26
  sheet: -2.55 (0.38), residues: 165
  loop : -3.40 (0.26), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP H  47 
 HIS   0.004   0.001   HIS L 198 
 PHE   0.033   0.003   PHE H  27 
 TYR   0.025   0.002   TYR L 140 
 ARG   0.011   0.001   ARG H  71 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.8956 (mp) cc_final: 0.8655 (mm)
REVERT: H   72 ASP cc_start: 0.8262 (t0) cc_final: 0.7824 (t0)
REVERT: H  144 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7986 (t0)
REVERT: L  110 VAL cc_start: 0.5554 (OUTLIER) cc_final: 0.5297 (p)
  outliers start: 22
  outliers final: 13
  residues processed: 93
  average time/residue: 0.2051
  time to fit residues: 24.2187
Evaluate side-chains
  86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain H residue  140 CYS
Chi-restraints excluded: chain H residue  144 ASP
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  189 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 9 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    0.1980
   chunk 59 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0370
   chunk 37 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.3258

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.093275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.084157 restraints weight = 22388.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.086325 restraints weight = 13135.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.087769 restraints weight = 8606.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3942 r_free = 0.3942    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3942 r_free = 0.3942    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6495
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4984  Z= 0.202
  Angle     :  0.772   7.533   6782  Z= 0.392
  Chirality :  0.048   0.160    763
  Planarity :  0.005   0.053    867
  Dihedral  :  7.247  57.974    777
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 14.94 %
    Favored  : 84.90 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.68 %
    Favored  : 74.77 %
  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: -4.36 (0.30), residues: 616
  helix: -3.27 (0.75), residues: 26
  sheet: -2.46 (0.39), residues: 167
  loop : -3.27 (0.26), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H  47 
 HIS   0.003   0.001   HIS L 198 
 PHE   0.035   0.002   PHE H  27 
 TYR   0.023   0.001   TYR L  49 
 ARG   0.007   0.001   ARG H  71 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.8926 (mp) cc_final: 0.8638 (mm)
REVERT: H   72 ASP cc_start: 0.8207 (t0) cc_final: 0.7823 (t0)
REVERT: L  110 VAL cc_start: 0.5323 (OUTLIER) cc_final: 0.5049 (p)
  outliers start: 19
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1784
  time to fit residues: 20.6143
Evaluate side-chains
  85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain H residue  140 CYS
Chi-restraints excluded: chain H residue  144 ASP
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  189 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0770
   chunk 49 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 60 optimal weight:    6.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
H  58 ASN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.093364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.084244 restraints weight = 22495.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.086376 restraints weight = 13267.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.087791 restraints weight = 8745.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3946 r_free = 0.3946    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3946 r_free = 0.3946    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6508
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4984  Z= 0.215
  Angle     :  0.766  10.133   6782  Z= 0.387
  Chirality :  0.049   0.370    763
  Planarity :  0.005   0.047    867
  Dihedral  :  6.833  57.124    777
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 17.21 %
    Favored  : 82.63 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 23.55 %
    Favored  : 73.83 %
  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: -4.25 (0.31), residues: 616
  helix: -3.30 (0.73), residues: 27
  sheet: -2.40 (0.39), residues: 172
  loop : -3.18 (0.27), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  47 
 HIS   0.003   0.001   HIS L 198 
 PHE   0.037   0.002   PHE H  27 
 TYR   0.020   0.001   TYR L 140 
 ARG   0.007   0.001   ARG H  71 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.8921 (mp) cc_final: 0.8643 (mm)
REVERT: H   72 ASP cc_start: 0.8149 (t0) cc_final: 0.7785 (t0)
REVERT: H  117 LYS cc_start: 0.7358 (pptt) cc_final: 0.6129 (pptt)
REVERT: H  144 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7385 (t0)
REVERT: L  110 VAL cc_start: 0.5348 (OUTLIER) cc_final: 0.5097 (p)
  outliers start: 14
  outliers final: 10
  residues processed: 83
  average time/residue: 0.2137
  time to fit residues: 22.5825
Evaluate side-chains
  85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain H residue  140 CYS
Chi-restraints excluded: chain H residue  144 ASP
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  189 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 4 optimal weight:    0.0980
   chunk 11 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0870
   chunk 31 optimal weight:    0.1980
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.093200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.084483 restraints weight = 22288.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.086516 restraints weight = 13402.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.087867 restraints weight = 8915.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3946 r_free = 0.3946    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3946 r_free = 0.3946    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.2931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4984  Z= 0.225
  Angle     :  0.756   7.679   6782  Z= 0.387
  Chirality :  0.048   0.305    763
  Planarity :  0.005   0.051    867
  Dihedral  :  6.670  56.981    777
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 16.72 %
    Favored  : 83.12 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.36 %
    Favored  : 73.64 %
  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: -4.21 (0.31), residues: 616
  helix: -3.23 (0.79), residues: 26
  sheet: -2.40 (0.39), residues: 173
  loop : -3.14 (0.27), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP H  47 
 HIS   0.003   0.001   HIS L 198 
 PHE   0.035   0.002   PHE H  27 
 TYR   0.019   0.001   TYR L 140 
 ARG   0.007   0.001   ARG H  71 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.8948 (mp) cc_final: 0.8665 (mm)
REVERT: H   72 ASP cc_start: 0.8255 (t0) cc_final: 0.7811 (t0)
REVERT: H  117 LYS cc_start: 0.7465 (pptt) cc_final: 0.6146 (pptt)
REVERT: H  144 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7395 (t0)
REVERT: L  110 VAL cc_start: 0.5553 (OUTLIER) cc_final: 0.5181 (p)
  outliers start: 16
  outliers final: 12
  residues processed: 81
  average time/residue: 0.1686
  time to fit residues: 17.5696
Evaluate side-chains
  86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain H residue  100 PHE
Chi-restraints excluded: chain H residue  140 CYS
Chi-restraints excluded: chain H residue  144 ASP
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  189 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 11 optimal weight:    0.4980
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.092657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.084270 restraints weight = 22400.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.086266 restraints weight = 13077.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.087573 restraints weight = 8518.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3916 r_free = 0.3916    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3916 r_free = 0.3916    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6563
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   4984  Z= 0.246
  Angle     :  0.772   8.685   6782  Z= 0.393
  Chirality :  0.049   0.290    763
  Planarity :  0.005   0.050    867
  Dihedral  :  6.603  56.221    777
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 17.53 %
    Favored  : 82.31 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 23.74 %
    Favored  : 73.64 %
  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: -4.28 (0.30), residues: 616
  helix: -3.13 (0.81), residues: 26
  sheet: -2.53 (0.38), residues: 171
  loop : -3.16 (0.27), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP H  47 
 HIS   0.003   0.001   HIS L 198 
 PHE   0.035   0.002   PHE H  27 
 TYR   0.020   0.002   TYR L  91 
 ARG   0.007   0.001   ARG H  71 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 ILE cc_start: 0.8982 (mp) cc_final: 0.8706 (mm)
REVERT: H   72 ASP cc_start: 0.8202 (t0) cc_final: 0.7806 (t0)
REVERT: H  117 LYS cc_start: 0.7540 (pptt) cc_final: 0.6210 (pptt)
REVERT: H  144 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7372 (t0)
REVERT: L  110 VAL cc_start: 0.5504 (OUTLIER) cc_final: 0.5264 (p)
REVERT: L  117 ILE cc_start: 0.7083 (tt) cc_final: 0.6624 (tp)
  outliers start: 14
  outliers final: 10
  residues processed: 81
  average time/residue: 0.1918
  time to fit residues: 19.5459
Evaluate side-chains
  84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain H residue  140 CYS
Chi-restraints excluded: chain H residue  144 ASP
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  189 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 47 optimal weight:    0.1980
   chunk 48 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.093311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.085157 restraints weight = 22982.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.086938 restraints weight = 14180.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.088155 restraints weight = 9672.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3932 r_free = 0.3932    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3932 r_free = 0.3932    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6548
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   4984  Z= 0.228
  Angle     :  0.769   8.378   6782  Z= 0.390
  Chirality :  0.048   0.274    763
  Planarity :  0.005   0.050    867
  Dihedral  :  6.546  57.479    777
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 15.75 %
    Favored  : 84.09 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 24.30 %
    Favored  : 73.46 %
  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: -4.27 (0.30), residues: 616
  helix: -3.17 (0.80), residues: 26
  sheet: -2.54 (0.38), residues: 171
  loop : -3.14 (0.27), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP H  47 
 HIS   0.003   0.001   HIS L 198 
 PHE   0.034   0.002   PHE H  27 
 TYR   0.012   0.001   TYR A 453 
 ARG   0.007   0.001   ARG H  71 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2296.07 seconds
wall clock time: 43 minutes 25.08 seconds (2605.08 seconds total)