Starting phenix.real_space_refine
on Wed Mar 12 02:05:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vyi_21461/03_2025/6vyi_21461.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vyi_21461/03_2025/6vyi_21461.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vyi_21461/03_2025/6vyi_21461.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vyi_21461/03_2025/6vyi_21461.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vyi_21461/03_2025/6vyi_21461.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vyi_21461/03_2025/6vyi_21461.cif"
  }
  resolution = 3.0
  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=   0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      42      5.16       5
     C    4620      2.51       5
     N    1136      2.21       5
     O    1114      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6916
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3360
          Classifications: {'peptide': 406}
          Link IDs: {'PTRANS': 18, 'TRANS': 387}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3360
          Classifications: {'peptide': 406}
          Link IDs: {'PTRANS': 18, 'TRANS': 387}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 147
          Unusual residues: {'6OU': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 49
          Unusual residues: {'6OU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.39, per 1000 atoms: 0.63
  Number of scatterers: 6916
  At special positions: 0
  Unit cell: (109.725, 91.575, 81.675, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P       4     15.00
     O    1114      8.00
     N    1136      7.00
     C    4620      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 867.7 milliseconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1564

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      78.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 77 through 81
      removed outlier: 3.627A  pdb=" N   GLY A  81 " --> pdb=" O   SER A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 113
      removed outlier: 3.505A  pdb=" N   CYS A  92 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   ARG A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   LEU A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 127
      removed outlier: 3.607A  pdb=" N   GLN A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   VAL A 121 " --> pdb=" O   PRO A 117 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASP A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 155
      removed outlier: 4.299A  pdb=" N   ASN A 141 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   VAL A 142 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 185
      Proline residue:  A 179  - end of helix
    Processing helix  chain 'A' and resid 190 through 226
      removed outlier: 3.693A  pdb=" N   ARG A 222 " --> pdb=" O   CYS A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 257
      removed outlier: 3.785A  pdb=" N   PHE A 257 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 300
    Processing helix  chain 'A' and resid 300 through 307
      removed outlier: 4.089A  pdb=" N   SER A 307 " --> pdb=" O   THR A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.838A  pdb=" N   LYS A 325 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   VAL A 328 " --> pdb=" O   LEU A 324 " (cutoff:3.500A)
      Proline residue:  A 329  - end of helix
    Processing helix  chain 'A' and resid 343 through 353
    Processing helix  chain 'A' and resid 369 through 375
    Processing helix  chain 'A' and resid 378 through 389
    Processing helix  chain 'A' and resid 390 through 396
    Processing helix  chain 'A' and resid 399 through 420
    Processing helix  chain 'A' and resid 428 through 448
      removed outlier: 3.700A  pdb=" N   THR A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ILE A 438 " --> pdb=" O   MET A 434 " (cutoff:3.500A)
      Proline residue:  A 439  - end of helix
    Processing helix  chain 'A' and resid 449 through 463
    Processing helix  chain 'A' and resid 465 through 479
      removed outlier: 3.717A  pdb=" N   VAL A 469 " --> pdb=" O   GLN A 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 81
      removed outlier: 3.626A  pdb=" N   GLY B  81 " --> pdb=" O   SER B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 113
      removed outlier: 3.505A  pdb=" N   CYS B  92 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   ARG B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   LEU B 103 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 127
      removed outlier: 3.606A  pdb=" N   GLN B 119 " --> pdb=" O   VAL B 115 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL B 121 " --> pdb=" O   PRO B 117 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASP B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 155
      removed outlier: 4.298A  pdb=" N   ASN B 141 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   VAL B 142 " --> pdb=" O   ILE B 138 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   PHE B 143 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 185
      Proline residue:  B 179  - end of helix
    Processing helix  chain 'B' and resid 190 through 226
      removed outlier: 3.693A  pdb=" N   ARG B 222 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 257
      removed outlier: 3.786A  pdb=" N   PHE B 257 " --> pdb=" O   TYR B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 300
    Processing helix  chain 'B' and resid 300 through 307
      removed outlier: 4.089A  pdb=" N   SER B 307 " --> pdb=" O   THR B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 343
      removed outlier: 3.838A  pdb=" N   LYS B 325 " --> pdb=" O   GLU B 321 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   VAL B 328 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      Proline residue:  B 329  - end of helix
    Processing helix  chain 'B' and resid 343 through 353
    Processing helix  chain 'B' and resid 369 through 375
    Processing helix  chain 'B' and resid 378 through 389
    Processing helix  chain 'B' and resid 390 through 396
    Processing helix  chain 'B' and resid 399 through 420
    Processing helix  chain 'B' and resid 428 through 448
      removed outlier: 3.699A  pdb=" N   THR B 432 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ILE B 438 " --> pdb=" O   MET B 434 " (cutoff:3.500A)
      Proline residue:  B 439  - end of helix
    Processing helix  chain 'B' and resid 449 through 463
    Processing helix  chain 'B' and resid 465 through 479
      removed outlier: 3.718A  pdb=" N   VAL B 469 " --> pdb=" O   GLN B 465 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1308 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: 1.72

  Time building geometry restraints manager: 2.09 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1018
        1.32 -     1.44: 2138
        1.44 -     1.56: 3894
        1.56 -     1.68: 8
        1.68 -     1.80: 68
  Bond restraints: 7126
  Sorted by residual:
  bond pdb=" O22 6OU A 502 "
       pdb=" P23 6OU A 502 "
    ideal  model  delta    sigma   weight residual
    1.643  1.557  0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" O22 6OU B 501 "
       pdb=" P23 6OU B 501 "
    ideal  model  delta    sigma   weight residual
    1.643  1.566  0.077 2.00e-02 2.50e+03 1.47e+01
  bond pdb=" O22 6OU A 501 "
       pdb=" P23 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.643  1.568  0.075 2.00e-02 2.50e+03 1.40e+01
  bond pdb=" O22 6OU A 503 "
       pdb=" P23 6OU A 503 "
    ideal  model  delta    sigma   weight residual
    1.643  1.573  0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" C27 6OU A 503 "
       pdb=" C28 6OU A 503 "
    ideal  model  delta    sigma   weight residual
    1.512  1.563 -0.051 2.00e-02 2.50e+03 6.57e+00
  ... (remaining 7121 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.49: 9555
        3.49 -     6.98: 79
        6.98 -    10.46: 3
       10.46 -    13.95: 6
       13.95 -    17.44: 5
  Bond angle restraints: 9648
  Sorted by residual:
  angle pdb=" C21 6OU A 502 "
        pdb=" O22 6OU A 502 "
        pdb=" P23 6OU A 502 "
      ideal   model   delta    sigma   weight residual
     117.17  134.61  -17.44 3.00e+00 1.11e-01 3.38e+01
  angle pdb=" C21 6OU A 501 "
        pdb=" O22 6OU A 501 "
        pdb=" P23 6OU A 501 "
      ideal   model   delta    sigma   weight residual
     117.17  134.50  -17.33 3.00e+00 1.11e-01 3.34e+01
  angle pdb=" O22 6OU A 503 "
        pdb=" P23 6OU A 503 "
        pdb=" O26 6OU A 503 "
      ideal   model   delta    sigma   weight residual
      93.95  110.09  -16.14 3.00e+00 1.11e-01 2.89e+01
  angle pdb=" C21 6OU B 501 "
        pdb=" O22 6OU B 501 "
        pdb=" P23 6OU B 501 "
      ideal   model   delta    sigma   weight residual
     117.17  131.43  -14.26 3.00e+00 1.11e-01 2.26e+01
  angle pdb=" O22 6OU B 501 "
        pdb=" P23 6OU B 501 "
        pdb=" O26 6OU B 501 "
      ideal   model   delta    sigma   weight residual
      93.95  108.05  -14.10 3.00e+00 1.11e-01 2.21e+01
  ... (remaining 9643 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.83: 4045
       34.83 -    69.66: 109
       69.66 -   104.49: 21
      104.49 -   139.31: 11
      139.31 -   174.14: 4
  Dihedral angle restraints: 4190
    sinusoidal: 1778
      harmonic: 2412
  Sorted by residual:
  dihedral pdb=" CA  GLY A  87 "
           pdb=" C   GLY A  87 "
           pdb=" N   ILE A  88 "
           pdb=" CA  ILE A  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.65   23.35     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  GLY B  87 "
           pdb=" C   GLY B  87 "
           pdb=" N   ILE B  88 "
           pdb=" CA  ILE B  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.67   23.33     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" C19 6OU B 501 "
           pdb=" C20 6OU B 501 "
           pdb=" C21 6OU B 501 "
           pdb=" O22 6OU B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.00  115.14 -174.14     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 4187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 751
       0.051 -    0.102: 242
       0.102 -    0.153: 35
       0.153 -    0.204: 1
       0.204 -    0.255: 3
  Chirality restraints: 1032
  Sorted by residual:
  chirality pdb=" C20 6OU A 503 "
            pdb=" C19 6OU A 503 "
            pdb=" C21 6OU A 503 "
            pdb=" O30 6OU A 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.60   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" C20 6OU B 501 "
            pdb=" C19 6OU B 501 "
            pdb=" C21 6OU B 501 "
            pdb=" O30 6OU B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.57   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" C20 6OU A 502 "
            pdb=" C19 6OU A 502 "
            pdb=" C21 6OU A 502 "
            pdb=" O30 6OU A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.56   -0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1029 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 296 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.76e+00
        pdb=" C   ILE A 296 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ILE A 296 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLN A 297 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 296 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   ILE B 296 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ILE B 296 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLN B 297 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 243 "    0.026 5.00e-02 4.00e+02   3.87e-02 2.40e+00
        pdb=" N   PRO B 244 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 244 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 244 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 284
        2.71 -     3.25: 7272
        3.25 -     3.80: 11658
        3.80 -     4.35: 14141
        4.35 -     4.90: 24318
  Nonbonded interactions: 57673
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 351 "
            pdb=" NH2 ARG A 358 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" OE1 GLU B 351 "
            pdb=" NH2 ARG B 358 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" O   GLU B 416 "
            pdb=" OG  SER B 420 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   GLU A 416 "
            pdb=" OG  SER A 420 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" ND2 ASN A 366 "
            pdb=" O   ASN B  84 "
     model   vdw
     2.218 3.120
  ... (remaining 57668 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 66 through 481 or resid 501))
  selection = chain 'B'
}

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:             0.700
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.760
  Find NCS groups from input model:        0.250
  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:10.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
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      :  0.010   0.086   7126  Z= 0.614
  Angle     :  0.941  17.441   9648  Z= 0.447
  Chirality :  0.048   0.255   1032
  Planarity :  0.005   0.039   1172
  Dihedral  : 19.278 174.143   2626
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.19 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.99 (0.26), residues: 804
  helix: -1.16 (0.19), residues: 592
  sheet:  None (None), residues: 0
  loop : -4.15 (0.33), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 334 
 HIS   0.005   0.001   HIS B 382 
 PHE   0.016   0.002   PHE B 338 
 TYR   0.015   0.002   TYR B 417 
 ARG   0.005   0.001   ARG A 272 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
REVERT: A  306 ASN cc_start: 0.8273 (m-40) cc_final: 0.7945 (m-40)
REVERT: A  404 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.6766 (mtm110)
REVERT: B  404 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.6777 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 1.3181
  time to fit residues: 164.3073
Evaluate side-chains
  92 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    7.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
A 119 GLN
A 162 GLN
A 239 HIS
** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 GLN
A 465 GLN
B 119 GLN
B 162 GLN
B 239 HIS
B 266 ASN
B 292 GLN
B 465 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.133957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.104768 restraints weight = 9387.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 1.94
r_work: 0.3065 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7126  Z= 0.234
  Angle     :  0.610   7.201   9648  Z= 0.307
  Chirality :  0.040   0.123   1032
  Planarity :  0.005   0.033   1172
  Dihedral  : 18.096 179.506   1082
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 11.20 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.29), residues: 804
  helix:  0.43 (0.21), residues: 596
  sheet:  None (None), residues: 0
  loop : -3.30 (0.35), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 340 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.028   0.002   PHE B 443 
 TYR   0.013   0.001   TYR B 211 
 ARG   0.002   0.000   ARG A 446 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A  404 ARG cc_start: 0.7485 (mtt-85) cc_final: 0.6450 (mtm110)
REVERT: A  425 MET cc_start: 0.8425 (mtt) cc_final: 0.8205 (mtp)
REVERT: B  102 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7520 (tpt90)
REVERT: B  316 TYR cc_start: 0.7563 (m-10) cc_final: 0.7337 (m-80)
REVERT: B  404 ARG cc_start: 0.7475 (mtt-85) cc_final: 0.6425 (mtm110)
  outliers start: 23
  outliers final: 4
  residues processed: 115
  average time/residue: 0.9583
  time to fit residues: 117.6015
Evaluate side-chains
  103 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain B residue  102 ARG
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  248 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 59 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.134576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.104562 restraints weight = 9541.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 2.01
r_work: 0.3079 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7126  Z= 0.232
  Angle     :  0.586   7.386   9648  Z= 0.293
  Chirality :  0.039   0.123   1032
  Planarity :  0.005   0.031   1172
  Dihedral  : 16.657 177.998   1082
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 13.45 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.30), residues: 804
  helix:  1.05 (0.22), residues: 598
  sheet:  None (None), residues: 0
  loop : -3.07 (0.36), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 340 
 HIS   0.004   0.001   HIS A 474 
 PHE   0.012   0.001   PHE B 338 
 TYR   0.012   0.001   TYR B 417 
 ARG   0.002   0.000   ARG B 424 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 124
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A  176 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8855 (tp)
REVERT: A  248 THR cc_start: 0.8941 (p) cc_final: 0.8739 (p)
REVERT: A  318 ARG cc_start: 0.7595 (mmp-170) cc_final: 0.7138 (ttm170)
REVERT: A  363 ASP cc_start: 0.8974 (p0) cc_final: 0.8478 (p0)
REVERT: A  400 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7485 (ttmt)
REVERT: A  404 ARG cc_start: 0.7434 (mtt-85) cc_final: 0.6433 (mtm110)
REVERT: B  176 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8846 (tp)
REVERT: B  248 THR cc_start: 0.8924 (p) cc_final: 0.8719 (p)
REVERT: B  363 ASP cc_start: 0.8977 (p0) cc_final: 0.8483 (p0)
REVERT: B  368 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8345 (pt0)
REVERT: B  404 ARG cc_start: 0.7437 (mtt-85) cc_final: 0.6408 (mtm110)
REVERT: B  425 MET cc_start: 0.8489 (mtt) cc_final: 0.8246 (mtp)
  outliers start: 31
  outliers final: 7
  residues processed: 137
  average time/residue: 0.9976
  time to fit residues: 145.4787
Evaluate side-chains
  114 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  402 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 45 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   chunk 72 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.140453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.108245 restraints weight = 9258.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.13
r_work: 0.3141 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7126  Z= 0.184
  Angle     :  0.566   7.398   9648  Z= 0.283
  Chirality :  0.038   0.121   1032
  Planarity :  0.004   0.039   1172
  Dihedral  : 16.018 179.884   1082
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 16.11 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.31), residues: 804
  helix:  1.36 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.95 (0.38), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 340 
 HIS   0.004   0.001   HIS A 474 
 PHE   0.029   0.001   PHE A 443 
 TYR   0.010   0.001   TYR B 211 
 ARG   0.003   0.000   ARG A 222 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A  224 LYS cc_start: 0.8698 (ttpp) cc_final: 0.7915 (tmmt)
REVERT: A  248 THR cc_start: 0.8784 (p) cc_final: 0.8558 (p)
REVERT: A  318 ARG cc_start: 0.7495 (mmp-170) cc_final: 0.7026 (ttm170)
REVERT: A  400 LYS cc_start: 0.7418 (ttmt) cc_final: 0.7072 (ttmt)
REVERT: A  404 ARG cc_start: 0.7165 (mtt-85) cc_final: 0.6165 (mtm110)
REVERT: B   73 ASP cc_start: 0.8307 (m-30) cc_final: 0.8020 (t0)
REVERT: B  224 LYS cc_start: 0.8681 (ttpp) cc_final: 0.7920 (tmmt)
REVERT: B  248 THR cc_start: 0.8786 (p) cc_final: 0.8553 (p)
REVERT: B  368 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8326 (pt0)
REVERT: B  400 LYS cc_start: 0.7511 (ttmt) cc_final: 0.7181 (ttmt)
REVERT: B  404 ARG cc_start: 0.7162 (mtt-85) cc_final: 0.6147 (mtm110)
REVERT: B  425 MET cc_start: 0.8362 (mtt) cc_final: 0.8124 (mtp)
  outliers start: 25
  outliers final: 8
  residues processed: 139
  average time/residue: 1.1276
  time to fit residues: 165.8495
Evaluate side-chains
  120 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 49 optimal weight:    9.9990
   chunk 41 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 246 ASN
A 266 ASN
A 292 GLN
B 162 GLN
B 246 ASN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.136742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.104269 restraints weight = 9233.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.11
r_work: 0.3100 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7126  Z= 0.368
  Angle     :  0.638   7.815   9648  Z= 0.318
  Chirality :  0.041   0.124   1032
  Planarity :  0.005   0.039   1172
  Dihedral  : 16.171 170.394   1082
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 17.37 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.31), residues: 804
  helix:  1.30 (0.22), residues: 596
  sheet:  None (None), residues: 0
  loop : -2.85 (0.39), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 340 
 HIS   0.004   0.001   HIS A 382 
 PHE   0.029   0.002   PHE B 443 
 TYR   0.015   0.001   TYR B 417 
 ARG   0.003   0.000   ARG B 358 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 103
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A  248 THR cc_start: 0.8797 (p) cc_final: 0.8577 (p)
REVERT: A  318 ARG cc_start: 0.7524 (mmp-170) cc_final: 0.7035 (ttm170)
REVERT: A  400 LYS cc_start: 0.7429 (ttmt) cc_final: 0.7109 (ttmt)
REVERT: A  404 ARG cc_start: 0.7232 (mtt-85) cc_final: 0.6291 (mtm110)
REVERT: B  248 THR cc_start: 0.8806 (p) cc_final: 0.8584 (p)
REVERT: B  368 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8478 (pt0)
REVERT: B  400 LYS cc_start: 0.7519 (ttmt) cc_final: 0.7163 (ttmt)
REVERT: B  404 ARG cc_start: 0.7194 (mtt-85) cc_final: 0.6186 (mtm110)
  outliers start: 36
  outliers final: 10
  residues processed: 126
  average time/residue: 1.0365
  time to fit residues: 138.7261
Evaluate side-chains
  103 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 4 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.139738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.107313 restraints weight = 9182.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.12
r_work: 0.3140 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7126  Z= 0.229
  Angle     :  0.595   8.066   9648  Z= 0.297
  Chirality :  0.039   0.121   1032
  Planarity :  0.004   0.036   1172
  Dihedral  : 15.743 170.720   1082
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 17.23 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.31), residues: 804
  helix:  1.48 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.82 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 340 
 HIS   0.004   0.001   HIS B 474 
 PHE   0.029   0.002   PHE A 443 
 TYR   0.011   0.001   TYR A 417 
 ARG   0.003   0.000   ARG B 358 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A  224 LYS cc_start: 0.8685 (ttpp) cc_final: 0.7919 (tmmt)
REVERT: A  248 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8597 (p)
REVERT: A  400 LYS cc_start: 0.7359 (ttmt) cc_final: 0.7058 (ttmt)
REVERT: A  404 ARG cc_start: 0.7202 (mtt-85) cc_final: 0.6235 (mtm110)
REVERT: B  224 LYS cc_start: 0.8686 (ttpp) cc_final: 0.7933 (tmmt)
REVERT: B  248 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8604 (p)
REVERT: B  368 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8398 (pt0)
REVERT: B  400 LYS cc_start: 0.7450 (ttmt) cc_final: 0.7147 (ttmt)
REVERT: B  404 ARG cc_start: 0.7223 (mtt-85) cc_final: 0.6210 (mtm110)
REVERT: B  425 MET cc_start: 0.8375 (mtt) cc_final: 0.8143 (mtp)
  outliers start: 31
  outliers final: 13
  residues processed: 124
  average time/residue: 1.0540
  time to fit residues: 138.7583
Evaluate side-chains
  112 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  300 MET
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0370
   chunk 5 optimal weight:    6.9990
   chunk 59 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   overall best weight:    1.7864

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.138180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.105885 restraints weight = 9096.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.10
r_work: 0.3129 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   7126  Z= 0.283
  Angle     :  0.613   7.942   9648  Z= 0.305
  Chirality :  0.041   0.130   1032
  Planarity :  0.004   0.034   1172
  Dihedral  : 15.643 167.981   1082
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 17.93 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.31), residues: 804
  helix:  1.46 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.77 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 340 
 HIS   0.004   0.001   HIS A 474 
 PHE   0.018   0.002   PHE B 443 
 TYR   0.013   0.001   TYR A 417 
 ARG   0.003   0.000   ARG A 281 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 0.761 
Fit side-chains
REVERT: A  224 LYS cc_start: 0.8669 (ttpp) cc_final: 0.7909 (tmmt)
REVERT: A  248 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8614 (p)
REVERT: A  368 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8405 (pt0)
REVERT: A  400 LYS cc_start: 0.7367 (ttmt) cc_final: 0.7069 (ttmt)
REVERT: A  404 ARG cc_start: 0.7228 (mtt-85) cc_final: 0.6293 (mtm110)
REVERT: B  224 LYS cc_start: 0.8671 (ttpp) cc_final: 0.7923 (tmmt)
REVERT: B  248 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8606 (p)
REVERT: B  368 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8373 (pt0)
REVERT: B  400 LYS cc_start: 0.7468 (ttmt) cc_final: 0.7148 (ttmt)
REVERT: B  404 ARG cc_start: 0.7250 (mtt-85) cc_final: 0.6238 (mtm110)
REVERT: B  425 MET cc_start: 0.8372 (mtt) cc_final: 0.8135 (mtp)
  outliers start: 34
  outliers final: 16
  residues processed: 124
  average time/residue: 1.0361
  time to fit residues: 136.3470
Evaluate side-chains
  119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  266 ASN
Chi-restraints excluded: chain B residue  300 MET
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.141967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.108812 restraints weight = 9182.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 2.19
r_work: 0.3150 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7126  Z= 0.190
  Angle     :  0.590   8.286   9648  Z= 0.296
  Chirality :  0.039   0.120   1032
  Planarity :  0.004   0.041   1172
  Dihedral  : 15.277 167.972   1082
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.75 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.31), residues: 804
  helix:  1.62 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.71 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 340 
 HIS   0.004   0.001   HIS B 474 
 PHE   0.030   0.002   PHE A 443 
 TYR   0.010   0.001   TYR A 417 
 ARG   0.003   0.000   ARG A 281 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7801 (t0)
REVERT: A  224 LYS cc_start: 0.8662 (ttpp) cc_final: 0.7872 (tmmt)
REVERT: A  248 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8531 (p)
REVERT: A  368 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8210 (pt0)
REVERT: A  400 LYS cc_start: 0.7400 (ttmt) cc_final: 0.7109 (ttmt)
REVERT: A  404 ARG cc_start: 0.7193 (mtt-85) cc_final: 0.6247 (mtm110)
REVERT: B  224 LYS cc_start: 0.8643 (ttpp) cc_final: 0.7871 (tmmt)
REVERT: B  248 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8531 (p)
REVERT: B  368 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8202 (pt0)
REVERT: B  400 LYS cc_start: 0.7467 (ttmt) cc_final: 0.7157 (ttmt)
REVERT: B  404 ARG cc_start: 0.7168 (mtt-85) cc_final: 0.6206 (mtm110)
  outliers start: 27
  outliers final: 12
  residues processed: 128
  average time/residue: 1.0172
  time to fit residues: 138.1791
Evaluate side-chains
  117 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 266 ASN
A 292 GLN
B 162 GLN
B 266 ASN
B 292 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.142810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.109414 restraints weight = 9322.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.23
r_work: 0.3155 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7126  Z= 0.194
  Angle     :  0.594   7.910   9648  Z= 0.293
  Chirality :  0.040   0.186   1032
  Planarity :  0.004   0.037   1172
  Dihedral  : 14.964 166.132   1082
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 19.75 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.31), residues: 804
  helix:  1.69 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.68 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 340 
 HIS   0.004   0.001   HIS B 474 
 PHE   0.031   0.002   PHE A 443 
 TYR   0.010   0.001   TYR B 417 
 ARG   0.003   0.000   ARG A 281 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7801 (t0)
REVERT: A  224 LYS cc_start: 0.8635 (ttpp) cc_final: 0.7838 (tmmt)
REVERT: A  248 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8482 (p)
REVERT: A  318 ARG cc_start: 0.7433 (mmp-170) cc_final: 0.7102 (ttm170)
REVERT: A  368 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8210 (pt0)
REVERT: A  400 LYS cc_start: 0.7385 (ttmt) cc_final: 0.7093 (ttmt)
REVERT: A  404 ARG cc_start: 0.7210 (mtt-85) cc_final: 0.6242 (mtm110)
REVERT: A  467 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8143 (mp)
REVERT: B  224 LYS cc_start: 0.8629 (ttpp) cc_final: 0.7831 (tmmt)
REVERT: B  248 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8481 (p)
REVERT: B  368 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8166 (pt0)
REVERT: B  400 LYS cc_start: 0.7450 (ttmt) cc_final: 0.7131 (ttmt)
REVERT: B  404 ARG cc_start: 0.7181 (mtt-85) cc_final: 0.6209 (mtm110)
  outliers start: 29
  outliers final: 12
  residues processed: 125
  average time/residue: 1.1781
  time to fit residues: 155.4359
Evaluate side-chains
  126 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  266 ASN
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  402 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0570
   chunk 69 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 292 GLN
B 162 GLN
B 292 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.140942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108695 restraints weight = 9377.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.15
r_work: 0.3165 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.165   7126  Z= 0.340
  Angle     :  1.248  59.200   9648  Z= 0.738
  Chirality :  0.042   0.254   1032
  Planarity :  0.004   0.035   1172
  Dihedral  : 14.956 166.120   1082
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.73 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.31), residues: 804
  helix:  1.71 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.66 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 340 
 HIS   0.004   0.001   HIS B 474 
 PHE   0.030   0.002   PHE B 443 
 TYR   0.010   0.001   TYR A 417 
 ARG   0.003   0.000   ARG B 427 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.696 
Fit side-chains
REVERT: A   73 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8019 (t0)
REVERT: A  224 LYS cc_start: 0.8618 (ttpp) cc_final: 0.7812 (tmmt)
REVERT: A  248 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8532 (p)
REVERT: A  318 ARG cc_start: 0.7463 (mmp-170) cc_final: 0.7087 (ttm170)
REVERT: A  368 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8333 (pt0)
REVERT: A  400 LYS cc_start: 0.7363 (ttmt) cc_final: 0.7062 (ttmt)
REVERT: A  404 ARG cc_start: 0.7270 (mtt-85) cc_final: 0.6288 (mtm110)
REVERT: A  467 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8338 (mp)
REVERT: B  224 LYS cc_start: 0.8614 (ttpp) cc_final: 0.7808 (tmmt)
REVERT: B  248 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8534 (p)
REVERT: B  368 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8304 (pt0)
REVERT: B  400 LYS cc_start: 0.7445 (ttmt) cc_final: 0.7117 (ttmt)
REVERT: B  404 ARG cc_start: 0.7255 (mtt-85) cc_final: 0.6264 (mtm110)
  outliers start: 25
  outliers final: 12
  residues processed: 120
  average time/residue: 1.1489
  time to fit residues: 145.6088
Evaluate side-chains
  126 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  377 TRP
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain B residue  300 MET
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  377 TRP
Chi-restraints excluded: chain B residue  467 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 35 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 59 optimal weight:    9.9990
   chunk 19 optimal weight:   40.0000
   chunk 64 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 162 GLN
A 292 GLN
B 162 GLN
B 292 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.142580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.109578 restraints weight = 9280.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.21
r_work: 0.3160 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.165   7126  Z= 0.340
  Angle     :  1.248  59.200   9648  Z= 0.738
  Chirality :  0.042   0.254   1032
  Planarity :  0.004   0.035   1172
  Dihedral  : 14.956 166.120   1082
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 21.43 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.31), residues: 804
  helix:  1.71 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.66 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 340 
 HIS   0.004   0.001   HIS B 474 
 PHE   0.030   0.002   PHE B 443 
 TYR   0.010   0.001   TYR A 417 
 ARG   0.003   0.000   ARG B 427 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4741.96 seconds
wall clock time: 81 minutes 48.53 seconds (4908.53 seconds total)