Starting phenix.real_space_refine
on Tue Mar  3 16:10:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9teo_55831/03_2026/9teo_55831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9teo_55831/03_2026/9teo_55831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9teo_55831/03_2026/9teo_55831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9teo_55831/03_2026/9teo_55831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9teo_55831/03_2026/9teo_55831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9teo_55831/03_2026/9teo_55831.cif"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      54      5.49       5
     S      18      5.16       5
     C    4029      2.51       5
     N    1200      2.21       5
     O    1383      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6686
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3540
          Classifications: {'peptide': 453}
          Link IDs: {'PTRANS': 28, 'TRANS': 424}
    Chain: "B"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 326
          Classifications: {'peptide': 41}
          Link IDs: {'PTRANS': 1, 'TRANS': 39}
    Chain: "E"
      Number of atoms: 563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 563
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "F"
      Number of atoms: 544
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 544
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "I"
      Number of atoms: 1711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1711
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 12, 'TRANS': 204}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "I"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1778  SG  CYS A 366      61.738  68.147  29.625  1.00107.09           S
  ATOM   1793  SG  CYS A 368      58.395  66.868  28.305  1.00124.57           S
  ATOM   1938  SG  CYS A 387      61.656  66.362  26.216  1.00112.94           S
  ATOM   5722  SG  CYS I 117      89.176  74.980  53.534  1.00 95.97           S
  ATOM   5860  SG  CYS I 135      88.304  78.685  53.018  1.00112.08           S
  ATOM   5870  SG  CYS I 137      85.511  76.183  53.776  1.00102.39           S

  Time building chain proxies: 1.30, per 1000 atoms: 0.19
  Number of scatterers: 6686
  At special positions: 0
  Unit cell: (120.84, 94.34, 87.98, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      18     16.00
     P      54     15.00
     O    1383      8.00
     N    1200      7.00
     C    4029      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 222.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 401 "
        pdb="ZN    ZN A 701 " - pdb=" SG  CYS A 366 "
        pdb="ZN    ZN A 701 " - pdb=" SG  CYS A 368 "
        pdb="ZN    ZN A 701 " - pdb=" SG  CYS A 387 "
      pdb="  ZN I 301 "
        pdb="ZN    ZN I 301 " - pdb=" NE2 HIS I 115 "
        pdb="ZN    ZN I 301 " - pdb=" SG  CYS I 135 "
        pdb="ZN    ZN I 301 " - pdb=" SG  CYS I 117 "
        pdb="ZN    ZN I 301 " - pdb=" SG  CYS I 137 "
      Number of angles added : 6


  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1306

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 7 sheets defined
      42.1% alpha, 23.2% beta
      26 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 140 through 163
    Processing helix  chain 'A' and resid 211 through 226
    Processing helix  chain 'A' and resid 243 through 254
    Processing helix  chain 'A' and resid 258 through 264
    Processing helix  chain 'A' and resid 273 through 282
    Processing helix  chain 'A' and resid 283 through 288
    Processing helix  chain 'A' and resid 331 through 343
    Processing helix  chain 'A' and resid 379 through 382
    Processing helix  chain 'A' and resid 409 through 426
    Processing helix  chain 'A' and resid 430 through 444
    Processing helix  chain 'A' and resid 453 through 481
      removed outlier: 4.224A  pdb=" N   ARG A 457 " --> pdb=" O   LYS A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 517
    Processing helix  chain 'A' and resid 540 through 545
    Processing helix  chain 'A' and resid 546 through 557
    Processing helix  chain 'A' and resid 575 through 578
    Processing helix  chain 'B' and resid 464 through 480
    Processing helix  chain 'B' and resid 485 through 502
    Processing helix  chain 'I' and resid 56 through 68
    Processing helix  chain 'I' and resid 127 through 131
    Processing helix  chain 'I' and resid 140 through 150
      removed outlier: 3.582A  pdb=" N   GLU I 150 " --> pdb=" O   ALA I 146 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 167 through 171
      removed outlier: 3.972A  pdb=" N   GLY I 171 " --> pdb=" O   PRO I 168 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 179 through 198
      removed outlier: 3.655A  pdb=" N   VAL I 185 " --> pdb=" O   THR I 181 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   HIS I 187 " --> pdb=" O   PHE I 183 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   GLU I 188 " --> pdb=" O   LYS I 184 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 185
    Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 297
      removed outlier: 5.561A  pdb=" N   LYS A 296 " --> pdb=" O   ILE A 307 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ILE A 307 " --> pdb=" O   LYS A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 366
    Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 375
    Processing sheet with id=AA5, first strand: chain 'I' and resid 27 through 36
      removed outlier: 9.428A  pdb=" N   GLY I  27 " --> pdb=" O   ARG I  51 " (cutoff:3.500A)
      removed outlier: 10.848A  pdb=" N   ARG I  51 " --> pdb=" O   GLY I  27 " (cutoff:3.500A)
      removed outlier: 9.938A  pdb=" N   PHE I  29 " --> pdb=" O   LYS I  49 " (cutoff:3.500A)
      removed outlier: 11.490A  pdb=" N   LYS I  49 " --> pdb=" O   PHE I  29 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   SER I  31 " --> pdb=" O   LEU I  47 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE I  83 " --> pdb=" O   THR I  54 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'I' and resid 122 through 124
      removed outlier: 7.763A  pdb=" N   HIS I 116 " --> pdb=" O   VAL I 123 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   LEU I 113 " --> pdb=" O   LEU I 109 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU I 109 " --> pdb=" O   LEU I 113 " (cutoff:3.500A)
      removed outlier: 11.328A  pdb=" N   ALA I  98 " --> pdb=" O   THR I 163 " (cutoff:3.500A)
      removed outlier: 12.443A  pdb=" N   THR I 163 " --> pdb=" O   ALA I  98 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   GLY I 100 " --> pdb=" O   THR I 161 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASP I 104 " --> pdb=" O   ALA I 157 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 122 through 124
      removed outlier: 7.763A  pdb=" N   HIS I 116 " --> pdb=" O   VAL I 123 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   LEU I 113 " --> pdb=" O   LEU I 109 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU I 109 " --> pdb=" O   LEU I 113 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU I 203 " --> pdb=" O   LEU I 235 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR I 233 " --> pdb=" O   ASN I 205 " (cutoff:3.500A)

    284 hydrogen bonds defined for protein.
    810 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      68 hydrogen bonds
      136 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 0.90 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: 1746
        1.33 -     1.45: 1501
        1.45 -     1.57: 3561
        1.57 -     1.69: 106
        1.69 -     1.81: 27
  Bond restraints: 6941
  Sorted by residual:
  bond pdb=" CB  LYS A 232 "
       pdb=" CG  LYS A 232 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.92e+00
  bond pdb=" O4'  DG F  24 "
       pdb=" C1'  DG F  24 "
    ideal  model  delta    sigma   weight residual
    1.414  1.395  0.019 2.00e-02 2.50e+03 9.20e-01
  bond pdb=" C3'  DT E  53 "
       pdb=" C2'  DT E  53 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 8.66e-01
  bond pdb=" C4'  DC F  27 "
       pdb=" O4'  DC F  27 "
    ideal  model  delta    sigma   weight residual
    1.450  1.432  0.018 2.00e-02 2.50e+03 8.47e-01
  bond pdb=" O4'  DT E  36 "
       pdb=" C1'  DT E  36 "
    ideal  model  delta    sigma   weight residual
    1.414  1.396  0.018 2.00e-02 2.50e+03 7.70e-01
  ... (remaining 6936 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 9462
        1.86 -     3.73: 146
        3.73 -     5.59: 9
        5.59 -     7.45: 3
        7.45 -     9.31: 1
  Bond angle restraints: 9621
  Sorted by residual:
  angle pdb=" CB  LYS A 232 "
        pdb=" CG  LYS A 232 "
        pdb=" CD  LYS A 232 "
      ideal   model   delta    sigma   weight residual
     111.30  120.61   -9.31 2.30e+00 1.89e-01 1.64e+01
  angle pdb=" CA  LYS A 232 "
        pdb=" CB  LYS A 232 "
        pdb=" CG  LYS A 232 "
      ideal   model   delta    sigma   weight residual
     114.10  121.21   -7.11 2.00e+00 2.50e-01 1.26e+01
  angle pdb=" C   ASN I  74 "
        pdb=" N   GLU I  75 "
        pdb=" CA  GLU I  75 "
      ideal   model   delta    sigma   weight residual
     121.54  126.28   -4.74 1.91e+00 2.74e-01 6.16e+00
  angle pdb=" CA  PRO A 519 "
        pdb=" C   PRO A 519 "
        pdb=" N   LYS A 520 "
      ideal   model   delta    sigma   weight residual
     114.74  116.89   -2.15 1.03e+00 9.43e-01 4.37e+00
  angle pdb=" C   ALA A 255 "
        pdb=" N   VAL A 256 "
        pdb=" CA  VAL A 256 "
      ideal   model   delta    sigma   weight residual
     122.59  121.11    1.48 7.20e-01 1.93e+00 4.21e+00
  ... (remaining 9616 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 3148
       17.89 -    35.78: 553
       35.78 -    53.67: 254
       53.67 -    71.56: 68
       71.56 -    89.45: 9
  Dihedral angle restraints: 4032
    sinusoidal: 2001
      harmonic: 2031
  Sorted by residual:
  dihedral pdb=" CB  GLU A 431 "
           pdb=" CG  GLU A 431 "
           pdb=" CD  GLU A 431 "
           pdb=" OE1 GLU A 431 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.45  -89.45     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A 183 "
           pdb=" CG  GLU A 183 "
           pdb=" CD  GLU A 183 "
           pdb=" OE1 GLU A 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.76   86.76     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CB  GLU A 439 "
           pdb=" CG  GLU A 439 "
           pdb=" CD  GLU A 439 "
           pdb=" OE1 GLU A 439 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.61  -86.61     1      3.00e+01 1.11e-03 1.00e+01
  ... (remaining 4029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 675
       0.028 -    0.056: 241
       0.056 -    0.085: 64
       0.085 -    0.113: 52
       0.113 -    0.141: 8
  Chirality restraints: 1040
  Sorted by residual:
  chirality pdb=" CG  LEU B 474 "
            pdb=" CB  LEU B 474 "
            pdb=" CD1 LEU B 474 "
            pdb=" CD2 LEU B 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.73    0.14 2.00e-01 2.50e+01 4.98e-01
  chirality pdb=" CA  ILE I  95 "
            pdb=" N   ILE I  95 "
            pdb=" C   ILE I  95 "
            pdb=" CB  ILE I  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.78e-01
  chirality pdb=" CA  ILE A 561 "
            pdb=" N   ILE A 561 "
            pdb=" C   ILE A 561 "
            pdb=" CB  ILE A 561 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1037 not shown)

  Planarity restraints: 1070
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 273 "    0.024 5.00e-02 4.00e+02   3.68e-02 2.17e+00
        pdb=" N   PRO A 274 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 274 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 274 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA I 153 "   -0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO I 154 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO I 154 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO I 154 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT E  38 "   -0.016 2.00e-02 2.50e+03   7.96e-03 1.58e+00
        pdb=" N1   DT E  38 "    0.017 2.00e-02 2.50e+03
        pdb=" C2   DT E  38 "    0.001 2.00e-02 2.50e+03
        pdb=" O2   DT E  38 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DT E  38 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DT E  38 "   -0.004 2.00e-02 2.50e+03
        pdb=" O4   DT E  38 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DT E  38 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT E  38 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DT E  38 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1067 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 3273
        2.99 -     3.47: 6767
        3.47 -     3.94: 11712
        3.94 -     4.42: 13270
        4.42 -     4.90: 19944
  Nonbonded interactions: 54966
  Sorted by model distance:
  nonbonded pdb=" O5'  DG E  48 "
            pdb=" O4'  DG E  48 "
     model   vdw
     2.512 2.432
  nonbonded pdb=" O5'  DG E  57 "
            pdb=" O4'  DG E  57 "
     model   vdw
     2.567 2.432
  nonbonded pdb=" N1   DG E  47 "
            pdb=" C4   DG E  47 "
     model   vdw
     2.595 2.672
  nonbonded pdb=" N1   DG E  32 "
            pdb=" C4   DG E  32 "
     model   vdw
     2.596 2.672
  nonbonded pdb=" N1   DG E  34 "
            pdb=" C4   DG E  34 "
     model   vdw
     2.596 2.672
  ... (remaining 54961 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:             3.360
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.280
  Find NCS groups from input model:        0.030
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5316
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   0.042   6949  Z= 0.150
  Angle     :  0.525   9.315   9627  Z= 0.292
  Chirality :  0.037   0.141   1040
  Planarity :  0.004   0.037   1070
  Dihedral  : 21.619  89.446   2726
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 22.34 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.32), residues: 705
  helix:  2.28 (0.30), residues: 270
  sheet: -1.03 (0.54), residues: 101
  loop :  0.01 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 189 
 TYR   0.008   0.001   TYR A 475 
 PHE   0.009   0.001   PHE A 444 
 TRP   0.009   0.001   TRP I 103 
 HIS   0.004   0.001   HIS I 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6941)
  covalent geometry    : angle       0.52387 ( 9621)
  hydrogen bonds       : bond        0.12448 (  347)
  hydrogen bonds       : angle       6.49764 (  946)
  metal coordination   : bond        0.01255 (    8)
  metal coordination   : angle       1.31306 (    6)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 155
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 ILE cc_start: 0.7336 (pt) cc_final: 0.6659 (pt)
REVERT: A  460 LEU cc_start: 0.7020 (mt) cc_final: 0.6716 (tp)
REVERT: A  468 LEU cc_start: 0.8162 (mt) cc_final: 0.7691 (mp)
REVERT: A  489 ARG cc_start: 0.6177 (ppt170) cc_final: 0.5967 (ppt170)
REVERT: B  471 LEU cc_start: 0.7941 (mt) cc_final: 0.7556 (mt)
REVERT: B  475 TYR cc_start: 0.7526 (m-80) cc_final: 0.7159 (m-80)
REVERT: B  476 GLU cc_start: 0.6919 (pt0) cc_final: 0.6574 (pt0)
REVERT: B  493 ARG cc_start: 0.8531 (mmt90) cc_final: 0.8269 (mtt90)
  outliers start: 4
  outliers final: 1
  residues processed: 157
  average time/residue: 0.1100
  time to fit residues: 21.4677
Evaluate side-chains
  90 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 426 HIS
** I  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.094911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.078273 restraints weight = 20982.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 3.00
r_work: 0.3385 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.7937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   6949  Z= 0.284
  Angle     :  0.901  12.792   9627  Z= 0.485
  Chirality :  0.048   0.180   1040
  Planarity :  0.007   0.076   1070
  Dihedral  : 22.404  75.521   1354
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 21.99 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.31), residues: 705
  helix:  0.74 (0.29), residues: 258
  sheet: -1.45 (0.47), residues: 132
  loop : -0.42 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG A 551 
 TYR   0.027   0.004   TYR I 238 
 PHE   0.026   0.004   PHE A 209 
 TRP   0.051   0.004   TRP A 584 
 HIS   0.019   0.003   HIS A 426 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 ( 6941)
  covalent geometry    : angle       0.89377 ( 9621)
  hydrogen bonds       : bond        0.05649 (  347)
  hydrogen bonds       : angle       5.46832 (  946)
  metal coordination   : bond        0.02966 (    8)
  metal coordination   : angle       4.53510 (    6)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 103
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6804 (pm20)
REVERT: A  343 ASP cc_start: 0.6706 (m-30) cc_final: 0.6235 (t70)
REVERT: A  464 ARG cc_start: 0.8323 (tmm-80) cc_final: 0.8054 (tpt90)
REVERT: A  527 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7618 (m-80)
REVERT: B  493 ARG cc_start: 0.8595 (mmt90) cc_final: 0.8359 (mtt90)
REVERT: B  501 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8656 (pp)
REVERT: I   82 PHE cc_start: 0.7289 (p90) cc_final: 0.6533 (p90)
REVERT: I  210 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5896 (tp)
  outliers start: 32
  outliers final: 7
  residues processed: 124
  average time/residue: 0.1110
  time to fit residues: 17.2489
Evaluate side-chains
  80 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  527 PHE
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain I residue   42 VAL
Chi-restraints excluded: chain I residue  210 LEU
Chi-restraints excluded: chain I residue  211 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 42 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 64 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0060
   chunk 4 optimal weight:    9.9990
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** I  81 ASN ** 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 = 0.3747 r_free = 0.3747 target = 0.090654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.072770 restraints weight = 19903.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.95
r_work: 0.3241 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.8991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6949  Z= 0.158
  Angle     :  0.625  13.459   9627  Z= 0.333
  Chirality :  0.040   0.145   1040
  Planarity :  0.004   0.048   1070
  Dihedral  : 22.007  80.379   1353
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 24.74 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.32), residues: 705
  helix:  1.40 (0.30), residues: 269
  sheet: -1.43 (0.46), residues: 129
  loop :  0.00 (0.38), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I  28 
 TYR   0.012   0.001   TYR I  33 
 PHE   0.017   0.002   PHE I  67 
 TRP   0.030   0.002   TRP A 220 
 HIS   0.004   0.001   HIS I 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6941)
  covalent geometry    : angle       0.62401 ( 9621)
  hydrogen bonds       : bond        0.03848 (  347)
  hydrogen bonds       : angle       4.84543 (  946)
  metal coordination   : bond        0.01314 (    8)
  metal coordination   : angle       1.51186 (    6)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 ASP cc_start: 0.7143 (m-30) cc_final: 0.6661 (t70)
REVERT: A  457 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7919 (ptm-80)
REVERT: B  471 LEU cc_start: 0.7438 (mt) cc_final: 0.6744 (mm)
REVERT: B  475 TYR cc_start: 0.7669 (m-80) cc_final: 0.7348 (m-80)
REVERT: I   52 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8611 (mm)
  outliers start: 13
  outliers final: 7
  residues processed: 79
  average time/residue: 0.1021
  time to fit residues: 10.3526
Evaluate side-chains
  68 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  452 GLU
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain I residue   52 ILE
Chi-restraints excluded: chain I residue  238 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 70 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0050
   chunk 65 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0670
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5134

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.089489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.070600 restraints weight = 19861.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.98
r_work: 0.3187 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          1.0396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6949  Z= 0.158
  Angle     :  0.613   9.411   9627  Z= 0.330
  Chirality :  0.040   0.161   1040
  Planarity :  0.004   0.040   1070
  Dihedral  : 21.782  79.024   1353
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 24.40 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.33), residues: 705
  helix:  1.61 (0.30), residues: 275
  sheet: -1.51 (0.45), residues: 135
  loop : -0.11 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 489 
 TYR   0.019   0.002   TYR I 228 
 PHE   0.021   0.002   PHE I  67 
 TRP   0.021   0.001   TRP A 220 
 HIS   0.004   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6941)
  covalent geometry    : angle       0.61152 ( 9621)
  hydrogen bonds       : bond        0.03585 (  347)
  hydrogen bonds       : angle       4.40872 (  946)
  metal coordination   : bond        0.01568 (    8)
  metal coordination   : angle       1.73745 (    6)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  308 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7844 (mt-10)
REVERT: A  437 LEU cc_start: 0.8873 (tp) cc_final: 0.8638 (tp)
REVERT: A  446 LYS cc_start: 0.8438 (tppt) cc_final: 0.8193 (tppt)
REVERT: A  457 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8070 (ptm-80)
REVERT: A  464 ARG cc_start: 0.8473 (tpt90) cc_final: 0.8252 (tpt90)
REVERT: A  471 LEU cc_start: 0.8187 (mt) cc_final: 0.7826 (mp)
REVERT: A  524 ASP cc_start: 0.7119 (p0) cc_final: 0.6338 (t70)
REVERT: B  471 LEU cc_start: 0.7538 (mt) cc_final: 0.6959 (mm)
REVERT: B  493 ARG cc_start: 0.8599 (mtt90) cc_final: 0.8198 (ptp90)
  outliers start: 21
  outliers final: 7
  residues processed: 79
  average time/residue: 0.1080
  time to fit residues: 10.8001
Evaluate side-chains
  62 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain A residue  558 VAL
Chi-restraints excluded: chain I residue  231 THR
Chi-restraints excluded: chain I residue  238 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 63 optimal weight:    0.1980
   chunk 15 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** I  81 ASN ** 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 = 0.3709 r_free = 0.3709 target = 0.088461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.069340 restraints weight = 19899.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.98
r_work: 0.3158 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          1.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6949  Z= 0.145
  Angle     :  0.590   9.763   9627  Z= 0.318
  Chirality :  0.039   0.131   1040
  Planarity :  0.004   0.041   1070
  Dihedral  : 21.743  81.216   1353
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 25.09 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.33), residues: 705
  helix:  1.74 (0.30), residues: 275
  sheet: -1.57 (0.50), residues: 118
  loop : -0.12 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 493 
 TYR   0.014   0.002   TYR A 483 
 PHE   0.020   0.002   PHE I  67 
 TRP   0.035   0.001   TRP A 438 
 HIS   0.003   0.001   HIS I 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6941)
  covalent geometry    : angle       0.58957 ( 9621)
  hydrogen bonds       : bond        0.03444 (  347)
  hydrogen bonds       : angle       4.42429 (  946)
  metal coordination   : bond        0.01156 (    8)
  metal coordination   : angle       0.86851 (    6)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  446 LYS cc_start: 0.8485 (tppt) cc_final: 0.8218 (tppt)
REVERT: A  457 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8251 (ptm-80)
REVERT: A  459 ASN cc_start: 0.8866 (t0) cc_final: 0.8335 (t0)
REVERT: A  464 ARG cc_start: 0.8442 (tpt90) cc_final: 0.7875 (tpt90)
REVERT: B  478 ARG cc_start: 0.7014 (ttm110) cc_final: 0.6751 (ttm110)
REVERT: I  221 ARG cc_start: 0.7410 (ptm160) cc_final: 0.6934 (mtt-85)
  outliers start: 15
  outliers final: 6
  residues processed: 66
  average time/residue: 0.1107
  time to fit residues: 9.1471
Evaluate side-chains
  58 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  372 MET
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain I residue   92 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.9788

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

Flipped N/Q/H residues before XYZ refinement:
** I  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.085643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.065941 restraints weight = 19823.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.94
r_work: 0.3098 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          1.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6949  Z= 0.207
  Angle     :  0.645   9.629   9627  Z= 0.345
  Chirality :  0.042   0.170   1040
  Planarity :  0.005   0.045   1070
  Dihedral  : 22.248  81.731   1353
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 26.98 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.33), residues: 705
  helix:  1.72 (0.30), residues: 276
  sheet: -1.66 (0.48), residues: 123
  loop : -0.12 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 493 
 TYR   0.021   0.002   TYR I 228 
 PHE   0.022   0.002   PHE I 141 
 TRP   0.025   0.002   TRP A 438 
 HIS   0.004   0.001   HIS I 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 6941)
  covalent geometry    : angle       0.64107 ( 9621)
  hydrogen bonds       : bond        0.03838 (  347)
  hydrogen bonds       : angle       4.55215 (  946)
  metal coordination   : bond        0.01916 (    8)
  metal coordination   : angle       2.87931 (    6)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A  422 ASN cc_start: 0.8900 (t0) cc_final: 0.8671 (t0)
REVERT: A  457 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8247 (ptm160)
REVERT: A  459 ASN cc_start: 0.9141 (t0) cc_final: 0.8609 (t0)
REVERT: A  464 ARG cc_start: 0.8620 (tpt90) cc_final: 0.7979 (tpt90)
REVERT: B  477 ASP cc_start: 0.6425 (p0) cc_final: 0.6179 (m-30)
REVERT: B  493 ARG cc_start: 0.8670 (mmt90) cc_final: 0.8162 (ptp90)
  outliers start: 13
  outliers final: 5
  residues processed: 59
  average time/residue: 0.1252
  time to fit residues: 9.1313
Evaluate side-chains
  47 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain I residue   92 VAL
Chi-restraints excluded: chain I residue  151 TYR
Chi-restraints excluded: chain I residue  216 LYS
Chi-restraints excluded: chain I residue  231 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0170
   chunk 26 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 42 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.9220

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

Flipped N/Q/H residues before XYZ refinement:
** I  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 222 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.082851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.063257 restraints weight = 19431.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 3.11
r_work: 0.2994 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          1.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6949  Z= 0.186
  Angle     :  0.611   9.805   9627  Z= 0.327
  Chirality :  0.041   0.207   1040
  Planarity :  0.004   0.051   1070
  Dihedral  : 21.946  81.084   1353
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 26.46 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.33), residues: 705
  helix:  1.83 (0.30), residues: 275
  sheet: -1.79 (0.51), residues: 112
  loop : -0.08 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 493 
 TYR   0.020   0.002   TYR I 228 
 PHE   0.014   0.002   PHE I 122 
 TRP   0.017   0.001   TRP A 438 
 HIS   0.002   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 6941)
  covalent geometry    : angle       0.60502 ( 9621)
  hydrogen bonds       : bond        0.03673 (  347)
  hydrogen bonds       : angle       4.50375 (  946)
  metal coordination   : bond        0.02042 (    8)
  metal coordination   : angle       3.33119 (    6)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  251 MET cc_start: 0.8654 (mtp) cc_final: 0.8170 (mtp)
REVERT: A  372 MET cc_start: 0.9038 (mtp) cc_final: 0.8568 (mtp)
REVERT: A  457 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8260 (ptm160)
REVERT: A  459 ASN cc_start: 0.9158 (t0) cc_final: 0.8654 (t0)
REVERT: A  464 ARG cc_start: 0.8539 (tpt90) cc_final: 0.8322 (tpt90)
REVERT: B  477 ASP cc_start: 0.6193 (p0) cc_final: 0.5939 (m-30)
REVERT: B  478 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6824 (ttm110)
  outliers start: 8
  outliers final: 4
  residues processed: 50
  average time/residue: 0.1269
  time to fit residues: 7.8924
Evaluate side-chains
  48 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain I residue  151 TYR
Chi-restraints excluded: chain I residue  222 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** I  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 222 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.082774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.063338 restraints weight = 19430.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 3.06
r_work: 0.2994 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          1.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6949  Z= 0.164
  Angle     :  0.590   9.398   9627  Z= 0.318
  Chirality :  0.040   0.198   1040
  Planarity :  0.004   0.047   1070
  Dihedral  : 21.880  80.661   1353
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 25.95 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.33), residues: 705
  helix:  1.89 (0.31), residues: 275
  sheet: -1.75 (0.51), residues: 112
  loop :  0.01 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 493 
 TYR   0.016   0.001   TYR I 228 
 PHE   0.012   0.002   PHE A 492 
 TRP   0.013   0.001   TRP A 438 
 HIS   0.002   0.001   HIS I 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6941)
  covalent geometry    : angle       0.58648 ( 9621)
  hydrogen bonds       : bond        0.03520 (  347)
  hydrogen bonds       : angle       4.40771 (  946)
  metal coordination   : bond        0.01463 (    8)
  metal coordination   : angle       2.62928 (    6)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  372 MET cc_start: 0.9045 (mtp) cc_final: 0.8604 (mtp)
REVERT: A  457 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8281 (ptm160)
REVERT: A  459 ASN cc_start: 0.9160 (t0) cc_final: 0.8643 (t0)
REVERT: A  464 ARG cc_start: 0.8444 (tpt90) cc_final: 0.8114 (ttt-90)
REVERT: B  475 TYR cc_start: 0.7448 (m-80) cc_final: 0.7080 (m-80)
REVERT: B  478 ARG cc_start: 0.7318 (ttm110) cc_final: 0.6840 (ttm110)
  outliers start: 7
  outliers final: 5
  residues processed: 48
  average time/residue: 0.1476
  time to fit residues: 8.6665
Evaluate side-chains
  47 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain I residue  151 TYR
Chi-restraints excluded: chain I residue  216 LYS
Chi-restraints excluded: chain I residue  222 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0980
   chunk 71 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0980
   chunk 62 optimal weight:    0.2980
   chunk 68 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
I  65 GLN
** I  81 ASN ** 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 = 0.3583 r_free = 0.3583 target = 0.082830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.063515 restraints weight = 19615.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 3.09
r_work: 0.2997 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          1.4101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6949  Z= 0.154
  Angle     :  0.586   9.282   9627  Z= 0.315
  Chirality :  0.039   0.220   1040
  Planarity :  0.004   0.045   1070
  Dihedral  : 21.811  80.265   1353
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 26.29 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.33), residues: 705
  helix:  1.94 (0.31), residues: 275
  sheet: -1.62 (0.56), residues: 96
  loop : -0.10 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  39 
 TYR   0.017   0.001   TYR I 228 
 PHE   0.012   0.001   PHE I 122 
 TRP   0.016   0.001   TRP A 438 
 HIS   0.002   0.001   HIS I 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6941)
  covalent geometry    : angle       0.58297 ( 9621)
  hydrogen bonds       : bond        0.03462 (  347)
  hydrogen bonds       : angle       4.40812 (  946)
  metal coordination   : bond        0.01330 (    8)
  metal coordination   : angle       2.35875 (    6)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A  372 MET cc_start: 0.9008 (mtp) cc_final: 0.8546 (mtp)
REVERT: A  457 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8550 (ptm160)
REVERT: A  459 ASN cc_start: 0.9188 (t0) cc_final: 0.8674 (t0)
REVERT: B  475 TYR cc_start: 0.7536 (m-80) cc_final: 0.7100 (m-80)
  outliers start: 7
  outliers final: 3
  residues processed: 47
  average time/residue: 0.1560
  time to fit residues: 8.9753
Evaluate side-chains
  45 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain I residue  151 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0060
   chunk 11 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0970
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.3394

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

Flipped N/Q/H residues before XYZ refinement:
I  65 GLN
** I  81 ASN ** 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 = 0.3689 r_free = 0.3689 target = 0.086559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.067668 restraints weight = 19709.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.88
r_work: 0.3142 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          1.4299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6949  Z= 0.130
  Angle     :  0.583   8.853   9627  Z= 0.311
  Chirality :  0.039   0.221   1040
  Planarity :  0.004   0.035   1070
  Dihedral  : 21.564  79.836   1353
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 26.63 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.33), residues: 705
  helix:  2.06 (0.31), residues: 275
  sheet: -1.76 (0.57), residues: 88
  loop : -0.03 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG I 217 
 TYR   0.016   0.001   TYR I 228 
 PHE   0.012   0.001   PHE I 122 
 TRP   0.011   0.001   TRP A 438 
 HIS   0.002   0.000   HIS I 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6941)
  covalent geometry    : angle       0.58110 ( 9621)
  hydrogen bonds       : bond        0.03270 (  347)
  hydrogen bonds       : angle       4.30004 (  946)
  metal coordination   : bond        0.00468 (    8)
  metal coordination   : angle       2.04061 (    6)

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

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

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1410 Ramachandran restraints generated.
    705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A  372 MET cc_start: 0.8834 (mtp) cc_final: 0.8463 (mtp)
REVERT: A  457 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8603 (ptm160)
REVERT: A  459 ASN cc_start: 0.9186 (t0) cc_final: 0.8670 (t0)
REVERT: B  478 ARG cc_start: 0.7038 (ttm110) cc_final: 0.6702 (ptp90)
REVERT: B  494 LYS cc_start: 0.9050 (tptp) cc_final: 0.8842 (tptp)
REVERT: I   95 ILE cc_start: 0.8719 (pt) cc_final: 0.8418 (tp)
REVERT: I  169 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8011 (pm20)
  outliers start: 5
  outliers final: 3
  residues processed: 54
  average time/residue: 0.1290
  time to fit residues: 8.6291
Evaluate side-chains
  49 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain I residue  151 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0270
   chunk 39 optimal weight:    0.6980
   chunk 34 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0070
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
** I  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  81 ASN ** 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 = 0.3679 r_free = 0.3679 target = 0.086247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.067338 restraints weight = 19616.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.88
r_work: 0.3136 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          1.4357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6949  Z= 0.130
  Angle     :  0.588  14.509   9627  Z= 0.310
  Chirality :  0.039   0.225   1040
  Planarity :  0.004   0.040   1070
  Dihedral  : 21.582  79.875   1353
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 27.32 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.33), residues: 705
  helix:  2.01 (0.31), residues: 275
  sheet: -1.68 (0.58), residues: 88
  loop :  0.01 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 464 
 TYR   0.031   0.002   TYR B 475 
 PHE   0.012   0.001   PHE I 122 
 TRP   0.013   0.001   TRP A 526 
 HIS   0.002   0.000   HIS I 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6941)
  covalent geometry    : angle       0.58648 ( 9621)
  hydrogen bonds       : bond        0.03315 (  347)
  hydrogen bonds       : angle       4.33436 (  946)
  metal coordination   : bond        0.00542 (    8)
  metal coordination   : angle       1.93781 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1640.92 seconds
wall clock time: 28 minutes 47.17 seconds (1727.17 seconds total)