Starting phenix.real_space_refine
on Wed Jun  3 18:08:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ii6_60591/06_2026/9ii6_60591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ii6_60591/06_2026/9ii6_60591.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/9ii6_60591/06_2026/9ii6_60591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ii6_60591/06_2026/9ii6_60591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ii6_60591/06_2026/9ii6_60591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ii6_60591/06_2026/9ii6_60591.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=   0.031
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       2      5.49       5
     S      36      5.16       5
     C    5045      2.51       5
     N    1404      2.21       5
     O    1488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7975
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 2016
          Classifications: {'peptide': 248}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 15, 'TRANS': 232}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1977
          Classifications: {'peptide': 239}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 225}
    Chain: "D"
      Number of atoms: 1966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1966
          Classifications: {'peptide': 238}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 223}
    Chain: "E"
      Number of atoms: 2001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 2001
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 15, 'TRANS': 231}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'H6P': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.15, per 1000 atoms: 0.27
  Number of scatterers: 7975
  At special positions: 0
  Unit cell: (95.7, 137.5, 145.2, 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      36     16.00
     P       2     15.00
     O    1488      8.00
     N    1404      7.00
     C    5045      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: 0.66
  Conformation dependent library (CDL) restraints added in 442.5 milliseconds
  

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1838

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 11 sheets defined
      22.5% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 246 through 262
      removed outlier: 3.855A  pdb=" N   PHE A 257 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 293
      removed outlier: 3.916A  pdb=" N   LEU A 266 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 291
    Processing helix  chain 'B' and resid 299 through 308
    Processing helix  chain 'B' and resid 316 through 320
      removed outlier: 3.609A  pdb=" N   THR B 319 " --> pdb=" O   ASP B 316 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 293
    Processing helix  chain 'D' and resid 299 through 308
      removed outlier: 3.848A  pdb=" N   LYS D 304 " --> pdb=" O   TYR D 300 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   MET D 305 " --> pdb=" O   HIS D 301 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA D 306 " --> pdb=" O   GLU D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 320
    Processing helix  chain 'E' and resid 247 through 253
    Processing helix  chain 'E' and resid 254 through 294
    Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 315
      removed outlier: 3.570A  pdb=" N   VAL A 322 " --> pdb=" O   ILE A 469 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE A 470 " --> pdb=" O   GLU A 363 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LEU A 297 " --> pdb=" O   ALA E 299 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   LEU E 297 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE E 470 " --> pdb=" O   GLU E 363 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL E 322 " --> pdb=" O   ILE E 469 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 489
      removed outlier: 6.619A  pdb=" N   PHE E 435 " --> pdb=" O   ILE E 444 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   THR E 446 " --> pdb=" O   VAL E 433 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   VAL E 433 " --> pdb=" O   THR E 446 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   LEU E 297 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LEU A 297 " --> pdb=" O   ALA E 299 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   VAL A 433 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   THR A 446 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   PHE A 435 " --> pdb=" O   ILE A 444 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU E 488 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348
      removed outlier: 3.816A  pdb=" N   TRP A 370 " --> pdb=" O   MET A 398 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 309 through 310
      removed outlier: 6.427A  pdb=" N   ASN B 446 " --> pdb=" O   HIS B 452 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   HIS B 452 " --> pdb=" O   ASN B 446 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 309 through 310
    Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326
    Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 356
      removed outlier: 3.585A  pdb=" N   THR B 414 " --> pdb=" O   THR B 420 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR B 420 " --> pdb=" O   THR B 414 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 324 through 326
    Processing sheet with id=AA9, first strand: chain 'D' and resid 354 through 355
      removed outlier: 3.758A  pdb=" N   PHE D 470 " --> pdb=" O   VAL D 355 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   TYR D 413 " --> pdb=" O   LEU D 423 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU D 423 " --> pdb=" O   TYR D 413 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 452 through 456
      removed outlier: 6.125A  pdb=" N   HIS D 453 " --> pdb=" O   ASN D 447 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   ASN D 447 " --> pdb=" O   HIS D 453 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   THR D 481 " --> pdb=" O   GLU D 371 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 346 through 348
      removed outlier: 3.858A  pdb=" N   TRP E 370 " --> pdb=" O   MET E 398 " (cutoff:3.500A)

    340 hydrogen bonds defined for protein.
    960 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: 1.12

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 1
        1.12 -     1.29: 1346
        1.29 -     1.47: 3211
        1.47 -     1.64: 3559
        1.64 -     1.82: 54
  Bond restraints: 8171
  Sorted by residual:
  bond pdb=" CG  PRO D 419 "
       pdb=" CD  PRO D 419 "
    ideal  model  delta    sigma   weight residual
    1.512  0.942  0.570 2.70e-02 1.37e+03 4.46e+02
  bond pdb=" N   PRO D 419 "
       pdb=" CD  PRO D 419 "
    ideal  model  delta    sigma   weight residual
    1.474  1.612 -0.138 1.40e-02 5.10e+03 9.67e+01
  bond pdb=" C27 H6P B 501 "
       pdb=" C30 H6P B 501 "
    ideal  model  delta    sigma   weight residual
    1.334  1.525 -0.191 2.00e-02 2.50e+03 9.11e+01
  bond pdb=" N   PRO D 419 "
       pdb=" CA  PRO D 419 "
    ideal  model  delta    sigma   weight residual
    1.468  1.362  0.106 1.70e-02 3.46e+03 3.85e+01
  bond pdb=" CB  PRO D 419 "
       pdb=" CG  PRO D 419 "
    ideal  model  delta    sigma   weight residual
    1.506  1.736 -0.230 3.90e-02 6.57e+02 3.49e+01
  ... (remaining 8166 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.03: 11010
        5.03 -    10.05: 30
       10.05 -    15.08: 10
       15.08 -    20.10: 2
       20.10 -    25.13: 1
  Bond angle restraints: 11053
  Sorted by residual:
  angle pdb=" N   PRO D 419 "
        pdb=" CD  PRO D 419 "
        pdb=" CG  PRO D 419 "
      ideal   model   delta    sigma   weight residual
     103.80   78.67   25.13 1.20e+00 6.94e-01 4.39e+02
  angle pdb=" CA  PRO D 419 "
        pdb=" N   PRO D 419 "
        pdb=" CD  PRO D 419 "
      ideal   model   delta    sigma   weight residual
     111.50   95.67   15.83 1.40e+00 5.10e-01 1.28e+02
  angle pdb=" N   PRO D 339 "
        pdb=" CD  PRO D 339 "
        pdb=" CG  PRO D 339 "
      ideal   model   delta    sigma   weight residual
     103.20   88.52   14.68 1.50e+00 4.44e-01 9.57e+01
  angle pdb=" CA  PRO D 339 "
        pdb=" N   PRO D 339 "
        pdb=" CD  PRO D 339 "
      ideal   model   delta    sigma   weight residual
     112.00  101.49   10.51 1.40e+00 5.10e-01 5.64e+01
  angle pdb=" CA  PRO D 419 "
        pdb=" CB  PRO D 419 "
        pdb=" CG  PRO D 419 "
      ideal   model   delta    sigma   weight residual
     104.00   89.95   14.05 1.90e+00 2.77e-01 5.47e+01
  ... (remaining 11048 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.06: 4611
       30.06 -    60.12: 329
       60.12 -    90.18: 21
       90.18 -   120.24: 0
      120.24 -   150.30: 2
  Dihedral angle restraints: 4963
    sinusoidal: 2128
      harmonic: 2835
  Sorted by residual:
  dihedral pdb=" CA  ARG A 293 "
           pdb=" C   ARG A 293 "
           pdb=" N   ARG A 294 "
           pdb=" CA  ARG A 294 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -140.27  -39.73     0      5.00e+00 4.00e-02 6.31e+01
  dihedral pdb=" CA  ARG A 294 "
           pdb=" C   ARG A 294 "
           pdb=" N   THR A 295 "
           pdb=" CA  THR A 295 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.67   25.33     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" O15 H6P B 501 "
           pdb=" O16 H6P B 501 "
           pdb=" P13 H6P B 501 "
           pdb=" P17 H6P B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     161.66   11.36  150.30     1      3.00e+01 1.11e-03 1.99e+01
  ... (remaining 4960 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 950
       0.057 -    0.115: 188
       0.115 -    0.172: 22
       0.172 -    0.229: 0
       0.229 -    0.287: 2
  Chirality restraints: 1162
  Sorted by residual:
  chirality pdb=" CA  PRO D 419 "
            pdb=" N   PRO D 419 "
            pdb=" C   PRO D 419 "
            pdb=" CB  PRO D 419 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CA  LYS A 267 "
            pdb=" N   LYS A 267 "
            pdb=" C   LYS A 267 "
            pdb=" CB  LYS A 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  LYS E 271 "
            pdb=" N   LYS E 271 "
            pdb=" C   LYS E 271 "
            pdb=" CB  LYS E 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.24e-01
  ... (remaining 1159 not shown)

  Planarity restraints: 1443
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C21 H6P B 501 "   -0.031 2.00e-02 2.50e+03   2.98e-01 1.11e+03
        pdb=" C27 H6P B 501 "    0.528 2.00e-02 2.50e+03
        pdb=" C28 H6P B 501 "   -0.256 2.00e-02 2.50e+03
        pdb=" C30 H6P B 501 "   -0.307 2.00e-02 2.50e+03
        pdb=" C31 H6P B 501 "    0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 418 "    0.068 5.00e-02 4.00e+02   9.33e-02 1.39e+01
        pdb=" N   PRO D 419 "   -0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO D 419 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO D 419 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 334 "   -0.060 5.00e-02 4.00e+02   9.06e-02 1.31e+01
        pdb=" N   PRO A 335 "    0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO A 335 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 335 "   -0.049 5.00e-02 4.00e+02
  ... (remaining 1440 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 990
        2.75 -     3.29: 7160
        3.29 -     3.83: 12546
        3.83 -     4.36: 14252
        4.36 -     4.90: 25191
  Nonbonded interactions: 60139
  Sorted by model distance:
  nonbonded pdb=" N   GLU B 328 "
            pdb=" OE1 GLU B 328 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" N   GLU A 485 "
            pdb=" OE1 GLU A 485 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OE2 GLU A 465 "
            pdb=" OG  SER A 467 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OE2 GLU B 272 "
            pdb=" NH1 ARG D 276 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" NE2 HIS E 443 "
            pdb=" OG1 THR E 446 "
     model   vdw
     2.281 3.120
  ... (remaining 60134 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 246 through 323 or (resid 324 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 325 through 396 or (resid 397 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 398 through 492))
  selection = (chain 'E' and (resid 246 through 370 or (resid 371 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 372 through 492))
}

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:             4.770
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.130
  Find NCS groups from input model:        0.110
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
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      :  0.009   0.570   8171  Z= 0.361
  Angle     :  0.955  25.130  11053  Z= 0.560
  Chirality :  0.046   0.287   1162
  Planarity :  0.010   0.298   1443
  Dihedral  : 18.366 150.305   3125
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.25 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 28.08 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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 (0.25), residues: 964
  helix:  2.38 (0.34), residues: 195
  sheet: -0.12 (0.32), residues: 223
  loop : -1.67 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 296 
 TYR   0.016   0.002   TYR D 455 
 PHE   0.027   0.002   PHE E 327 
 TRP   0.021   0.002   TRP D 303 
 HIS   0.005   0.001   HIS D 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00870 /  0.36 ( 8171)
  covalent geometry    : angle       0.95532 /  0.56 (11053)
  hydrogen bonds       : bond        0.14494 /  9.08 (  332)
  hydrogen bonds       : angle       6.31583 /  4.63 (  960)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 ARG cc_start: 0.8450 (mmm160) cc_final: 0.8011 (tpp-160)
REVERT: A  290 LEU cc_start: 0.8595 (tp) cc_final: 0.8283 (tt)
  outliers start: 2
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1377
  time to fit residues: 15.3134
Evaluate side-chains
  52 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B 330 GLN
** E 310 HIS ** 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 = 0.3663 r_free = 0.3663 target = 0.072956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.048795 restraints weight = 37635.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 4.55
r_work: 0.2815 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8171  Z= 0.165
  Angle     :  0.651   7.359  11053  Z= 0.343
  Chirality :  0.043   0.148   1162
  Planarity :  0.005   0.063   1443
  Dihedral  :  7.694 109.240   1093
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.05 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 23.48 %
    Favored  : 73.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.33 (0.26), residues: 964
  helix:  2.90 (0.34), residues: 189
  sheet: -0.07 (0.33), residues: 221
  loop : -1.49 (0.24), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 352 
 TYR   0.012   0.001   TYR B 466 
 PHE   0.014   0.001   PHE D 349 
 TRP   0.020   0.002   TRP B 303 
 HIS   0.004   0.001   HIS B 297 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.17 ( 8171)
  covalent geometry    : angle       0.65141 /  0.34 (11053)
  hydrogen bonds       : bond        0.05981 /  3.86 (  332)
  hydrogen bonds       : angle       5.31230 /  3.83 (  960)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8694 (tm-30)
REVERT: A  398 MET cc_start: 0.9072 (ttm) cc_final: 0.8765 (ttm)
REVERT: B  269 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8450 (tmm)
REVERT: B  376 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9009 (mmtp)
REVERT: D  264 MET cc_start: 0.8286 (ppp) cc_final: 0.8012 (ptt)
REVERT: D  447 ASN cc_start: 0.7316 (t0) cc_final: 0.7108 (t0)
REVERT: E  259 ARG cc_start: 0.7919 (mmt180) cc_final: 0.7655 (mmp80)
  outliers start: 28
  outliers final: 13
  residues processed: 81
  average time/residue: 0.0994
  time to fit residues: 10.8856
Evaluate side-chains
  64 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  323 ILE
Chi-restraints excluded: chain B residue  376 LYS
Chi-restraints excluded: chain D residue  366 HIS
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  416 LEU
Chi-restraints excluded: chain D residue  444 SER
Chi-restraints excluded: chain E residue  300 VAL
Chi-restraints excluded: chain E residue  325 CYS
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  395 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0000
   chunk 51 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0970
   chunk 3 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
** D 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 310 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.073394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.049354 restraints weight = 36920.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 4.50
r_work: 0.2844 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8171  Z= 0.120
  Angle     :  0.579   7.465  11053  Z= 0.305
  Chirality :  0.042   0.142   1162
  Planarity :  0.004   0.049   1443
  Dihedral  :  6.754  81.477   1093
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  3.73 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 23.71 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.13 (0.26), residues: 964
  helix:  3.15 (0.34), residues: 193
  sheet: -0.01 (0.33), residues: 228
  loop : -1.40 (0.24), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 375 
 TYR   0.009   0.001   TYR B 466 
 PHE   0.009   0.001   PHE B 434 
 TRP   0.019   0.001   TRP B 303 
 HIS   0.003   0.001   HIS D 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 8171)
  covalent geometry    : angle       0.57907 /  0.31 (11053)
  hydrogen bonds       : bond        0.05250 /  3.38 (  332)
  hydrogen bonds       : angle       4.90482 /  3.52 (  960)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8674 (tm-30)
REVERT: A  398 MET cc_start: 0.8917 (ttm) cc_final: 0.8590 (ttm)
REVERT: B  264 MET cc_start: 0.9294 (tmm) cc_final: 0.9056 (tmm)
REVERT: B  376 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8958 (mmtp)
REVERT: D  264 MET cc_start: 0.8390 (ppp) cc_final: 0.8156 (ptt)
REVERT: D  447 ASN cc_start: 0.7376 (t0) cc_final: 0.7070 (t0)
REVERT: E  255 LYS cc_start: 0.7180 (mttm) cc_final: 0.6630 (ttpp)
REVERT: E  283 LYS cc_start: 0.9213 (tttt) cc_final: 0.9005 (tptt)
REVERT: E  325 CYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8328 (t)
  outliers start: 21
  outliers final: 7
  residues processed: 73
  average time/residue: 0.0960
  time to fit residues: 9.6992
Evaluate side-chains
  59 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  376 LYS
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain D residue  366 HIS
Chi-restraints excluded: chain D residue  382 VAL
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain E residue  325 CYS
Chi-restraints excluded: chain E residue  367 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0170
   chunk 73 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 89 optimal weight:    0.0000
   chunk 41 optimal weight:    0.9990
   chunk 68 optimal weight:    9.9990
   chunk 67 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.5624

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

Flipped N/Q/H residues before XYZ refinement:
** D 453 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 = 0.3680 r_free = 0.3680 target = 0.073162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.049110 restraints weight = 37934.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 4.55
r_work: 0.2837 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8171  Z= 0.117
  Angle     :  0.560   7.370  11053  Z= 0.296
  Chirality :  0.043   0.155   1162
  Planarity :  0.004   0.041   1443
  Dihedral  :  5.610  46.276   1093
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  3.63 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.13 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.09 (0.26), residues: 964
  helix:  3.18 (0.33), residues: 193
  sheet: -0.02 (0.33), residues: 232
  loop : -1.37 (0.25), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 348 
 TYR   0.009   0.001   TYR B 466 
 PHE   0.026   0.001   PHE D 349 
 TRP   0.019   0.001   TRP B 303 
 HIS   0.004   0.001   HIS D 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 8171)
  covalent geometry    : angle       0.56006 /  0.30 (11053)
  hydrogen bonds       : bond        0.04932 /  3.19 (  332)
  hydrogen bonds       : angle       4.77394 /  3.42 (  960)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 ARG cc_start: 0.8504 (mmp80) cc_final: 0.8293 (tpp-160)
REVERT: A  289 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8656 (tm-30)
REVERT: A  398 MET cc_start: 0.8934 (ttm) cc_final: 0.8577 (ttm)
REVERT: A  464 CYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8193 (p)
REVERT: B  264 MET cc_start: 0.9297 (tmm) cc_final: 0.9078 (tmm)
REVERT: D  447 ASN cc_start: 0.7445 (t0) cc_final: 0.7066 (t0)
REVERT: E  259 ARG cc_start: 0.7605 (mmt180) cc_final: 0.7065 (mmp80)
REVERT: E  263 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8252 (mp0)
REVERT: E  283 LYS cc_start: 0.9190 (tttt) cc_final: 0.8953 (tptt)
REVERT: E  325 CYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8454 (t)
  outliers start: 19
  outliers final: 11
  residues processed: 71
  average time/residue: 0.1046
  time to fit residues: 10.1451
Evaluate side-chains
  59 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain D residue  366 HIS
Chi-restraints excluded: chain D residue  382 VAL
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain E residue  263 GLU
Chi-restraints excluded: chain E residue  325 CYS
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  395 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** D 453 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 = 0.3652 r_free = 0.3652 target = 0.072002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.048029 restraints weight = 37762.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 4.47
r_work: 0.2804 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8171  Z= 0.155
  Angle     :  0.582   7.379  11053  Z= 0.308
  Chirality :  0.043   0.154   1162
  Planarity :  0.005   0.044   1443
  Dihedral  :  5.498  55.613   1093
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  3.94 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 22.44 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.15 (0.26), residues: 964
  helix:  3.05 (0.34), residues: 193
  sheet: -0.08 (0.33), residues: 221
  loop : -1.34 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 273 
 TYR   0.011   0.001   TYR B 466 
 PHE   0.017   0.001   PHE D 349 
 TRP   0.032   0.001   TRP D 303 
 HIS   0.003   0.001   HIS D 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 ( 8171)
  covalent geometry    : angle       0.58211 /  0.31 (11053)
  hydrogen bonds       : bond        0.05244 /  3.43 (  332)
  hydrogen bonds       : angle       4.93400 /  3.52 (  960)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 48
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 ARG cc_start: 0.8393 (mmp80) cc_final: 0.8155 (tpp-160)
REVERT: A  289 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8680 (tm-30)
REVERT: A  398 MET cc_start: 0.9017 (ttm) cc_final: 0.8638 (ttm)
REVERT: A  464 CYS cc_start: 0.8545 (t) cc_final: 0.8171 (p)
REVERT: B  264 MET cc_start: 0.9328 (tmm) cc_final: 0.9103 (tmm)
REVERT: B  376 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8976 (mmtp)
REVERT: D  289 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.9066 (tm-30)
REVERT: E  259 ARG cc_start: 0.7710 (mmt180) cc_final: 0.7461 (mmp80)
REVERT: E  325 CYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8571 (t)
  outliers start: 24
  outliers final: 16
  residues processed: 71
  average time/residue: 0.0989
  time to fit residues: 9.7399
Evaluate side-chains
  65 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 45
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  328 ARG
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  376 LYS
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain D residue  289 GLN
Chi-restraints excluded: chain D residue  366 HIS
Chi-restraints excluded: chain D residue  382 VAL
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  470 PHE
Chi-restraints excluded: chain D residue  473 LEU
Chi-restraints excluded: chain E residue  263 GLU
Chi-restraints excluded: chain E residue  325 CYS
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  395 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
D 453 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.072428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.048477 restraints weight = 37861.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 4.46
r_work: 0.2820 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8171  Z= 0.124
  Angle     :  0.567   8.718  11053  Z= 0.296
  Chirality :  0.042   0.150   1162
  Planarity :  0.004   0.046   1443
  Dihedral  :  4.828  37.363   1093
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  3.53 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.01 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.10 (0.26), residues: 964
  helix:  3.19 (0.34), residues: 193
  sheet: -0.10 (0.33), residues: 222
  loop : -1.33 (0.25), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 259 
 TYR   0.009   0.001   TYR B 466 
 PHE   0.012   0.001   PHE D 457 
 TRP   0.035   0.001   TRP D 303 
 HIS   0.003   0.001   HIS D 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.12 ( 8171)
  covalent geometry    : angle       0.56742 /  0.30 (11053)
  hydrogen bonds       : bond        0.04897 /  3.18 (  332)
  hydrogen bonds       : angle       4.80131 /  3.44 (  960)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 51
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8710 (tm-30)
REVERT: A  359 TYR cc_start: 0.9390 (p90) cc_final: 0.9000 (p90)
REVERT: A  398 MET cc_start: 0.8958 (ttm) cc_final: 0.8573 (ttm)
REVERT: A  464 CYS cc_start: 0.8578 (t) cc_final: 0.8220 (p)
REVERT: B  264 MET cc_start: 0.9322 (tmm) cc_final: 0.9091 (tmm)
REVERT: B  376 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9005 (mmtp)
REVERT: D  289 GLN cc_start: 0.9373 (tm-30) cc_final: 0.9120 (tm-30)
REVERT: D  305 MET cc_start: 0.9083 (mpp) cc_final: 0.8855 (pmm)
REVERT: E  259 ARG cc_start: 0.7676 (mmt180) cc_final: 0.7455 (mmp80)
REVERT: E  325 CYS cc_start: 0.8843 (OUTLIER) cc_final: 0.7968 (t)
  outliers start: 24
  outliers final: 16
  residues processed: 73
  average time/residue: 0.0795
  time to fit residues: 8.5251
Evaluate side-chains
  63 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  376 LYS
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain D residue  301 HIS
Chi-restraints excluded: chain D residue  366 HIS
Chi-restraints excluded: chain D residue  382 VAL
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  444 SER
Chi-restraints excluded: chain D residue  470 PHE
Chi-restraints excluded: chain D residue  473 LEU
Chi-restraints excluded: chain E residue  263 GLU
Chi-restraints excluded: chain E residue  325 CYS
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  395 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** D 301 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 = 0.3659 r_free = 0.3659 target = 0.072340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.048361 restraints weight = 37980.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 4.44
r_work: 0.2816 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8171  Z= 0.134
  Angle     :  0.574   9.281  11053  Z= 0.299
  Chirality :  0.042   0.150   1162
  Planarity :  0.004   0.048   1443
  Dihedral  :  4.757  36.778   1093
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.25 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 22.90 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.05 (0.26), residues: 964
  helix:  3.21 (0.35), residues: 193
  sheet:  0.01 (0.34), residues: 216
  loop : -1.31 (0.25), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 331 
 TYR   0.010   0.001   TYR B 466 
 PHE   0.010   0.001   PHE D 457 
 TRP   0.034   0.001   TRP D 303 
 HIS   0.003   0.001   HIS D 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.13 ( 8171)
  covalent geometry    : angle       0.57400 /  0.30 (11053)
  hydrogen bonds       : bond        0.04958 /  3.24 (  332)
  hydrogen bonds       : angle       4.83328 /  3.45 (  960)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 44
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8689 (tm-30)
REVERT: A  398 MET cc_start: 0.8962 (ttm) cc_final: 0.8572 (ttm)
REVERT: A  464 CYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8190 (p)
REVERT: B  264 MET cc_start: 0.9320 (tmm) cc_final: 0.9095 (tmm)
REVERT: B  376 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8987 (mmtp)
REVERT: D  289 GLN cc_start: 0.9375 (tm-30) cc_final: 0.9134 (tm-30)
REVERT: D  305 MET cc_start: 0.9084 (mpp) cc_final: 0.8873 (pmm)
REVERT: E  259 ARG cc_start: 0.7661 (mmt180) cc_final: 0.7431 (mmp80)
REVERT: E  325 CYS cc_start: 0.8873 (OUTLIER) cc_final: 0.7949 (t)
  outliers start: 29
  outliers final: 21
  residues processed: 71
  average time/residue: 0.0754
  time to fit residues: 7.8982
Evaluate side-chains
  68 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  376 LYS
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain D residue  249 ILE
Chi-restraints excluded: chain D residue  301 HIS
Chi-restraints excluded: chain D residue  366 HIS
Chi-restraints excluded: chain D residue  382 VAL
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  444 SER
Chi-restraints excluded: chain D residue  470 PHE
Chi-restraints excluded: chain D residue  473 LEU
Chi-restraints excluded: chain E residue  263 GLU
Chi-restraints excluded: chain E residue  325 CYS
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  395 THR
Chi-restraints excluded: chain E residue  422 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 56 optimal weight:    0.1980
   chunk 65 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0970
   chunk 38 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0030
   chunk 2 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
** D 301 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 = 0.3675 r_free = 0.3675 target = 0.072976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.049177 restraints weight = 37752.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 4.43
r_work: 0.2840 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8171  Z= 0.108
  Angle     :  0.566   8.979  11053  Z= 0.292
  Chirality :  0.042   0.153   1162
  Planarity :  0.004   0.048   1443
  Dihedral  :  4.628  37.127   1093
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  3.84 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.25 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  0.04 (0.26), residues: 964
  helix:  3.28 (0.34), residues: 193
  sheet:  0.24 (0.34), residues: 212
  loop : -1.33 (0.25), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 352 
 TYR   0.013   0.001   TYR D 290 
 PHE   0.010   0.001   PHE D 457 
 TRP   0.034   0.001   TRP D 303 
 HIS   0.002   0.001   HIS D 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 ( 8171)
  covalent geometry    : angle       0.56611 /  0.29 (11053)
  hydrogen bonds       : bond        0.04548 /  2.95 (  332)
  hydrogen bonds       : angle       4.68215 /  3.35 (  960)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 47
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8704 (tm-30)
REVERT: A  464 CYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8193 (p)
REVERT: B  259 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8804 (mp10)
REVERT: B  264 MET cc_start: 0.9326 (tmm) cc_final: 0.9094 (tmm)
REVERT: B  376 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8963 (mmtp)
REVERT: D  289 GLN cc_start: 0.9363 (tm-30) cc_final: 0.9134 (tm-30)
REVERT: E  259 ARG cc_start: 0.7610 (mmt180) cc_final: 0.7377 (mmp80)
REVERT: E  325 CYS cc_start: 0.8826 (OUTLIER) cc_final: 0.7961 (t)
  outliers start: 25
  outliers final: 19
  residues processed: 69
  average time/residue: 0.0803
  time to fit residues: 8.1443
Evaluate side-chains
  70 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 47
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  376 LYS
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain D residue  249 ILE
Chi-restraints excluded: chain D residue  301 HIS
Chi-restraints excluded: chain D residue  366 HIS
Chi-restraints excluded: chain D residue  382 VAL
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  444 SER
Chi-restraints excluded: chain D residue  470 PHE
Chi-restraints excluded: chain D residue  473 LEU
Chi-restraints excluded: chain E residue  263 GLU
Chi-restraints excluded: chain E residue  325 CYS
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  395 THR
Chi-restraints excluded: chain E residue  422 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0670
   chunk 65 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 13 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.6518

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.072691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.049101 restraints weight = 36771.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 4.34
r_work: 0.2837 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8171  Z= 0.118
  Angle     :  0.571   8.899  11053  Z= 0.295
  Chirality :  0.042   0.150   1162
  Planarity :  0.004   0.048   1443
  Dihedral  :  4.613  36.407   1093
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  3.94 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.01 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  0.08 (0.27), residues: 964
  helix:  3.37 (0.34), residues: 193
  sheet:  0.15 (0.34), residues: 216
  loop : -1.28 (0.25), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 259 
 TYR   0.014   0.001   TYR D 290 
 PHE   0.010   0.001   PHE B 252 
 TRP   0.036   0.001   TRP D 303 
 HIS   0.003   0.001   HIS D 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 8171)
  covalent geometry    : angle       0.57074 /  0.30 (11053)
  hydrogen bonds       : bond        0.04573 /  2.98 (  332)
  hydrogen bonds       : angle       4.68599 /  3.34 (  960)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 48
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8700 (tm-30)
REVERT: A  464 CYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8248 (p)
REVERT: B  259 GLN cc_start: 0.9246 (mm-40) cc_final: 0.8863 (mp10)
REVERT: B  264 MET cc_start: 0.9305 (tmm) cc_final: 0.9094 (tmm)
REVERT: B  376 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8970 (mmtp)
REVERT: D  289 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9148 (tm-30)
REVERT: E  259 ARG cc_start: 0.7504 (mmt180) cc_final: 0.7273 (mmp80)
REVERT: E  325 CYS cc_start: 0.8875 (OUTLIER) cc_final: 0.7974 (t)
  outliers start: 26
  outliers final: 20
  residues processed: 72
  average time/residue: 0.0803
  time to fit residues: 8.4483
Evaluate side-chains
  72 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 48
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  376 LYS
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain D residue  249 ILE
Chi-restraints excluded: chain D residue  301 HIS
Chi-restraints excluded: chain D residue  366 HIS
Chi-restraints excluded: chain D residue  382 VAL
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  444 SER
Chi-restraints excluded: chain D residue  470 PHE
Chi-restraints excluded: chain D residue  473 LEU
Chi-restraints excluded: chain E residue  263 GLU
Chi-restraints excluded: chain E residue  325 CYS
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  395 THR
Chi-restraints excluded: chain E residue  422 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0970
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.3980
   chunk 79 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.072636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.048890 restraints weight = 36589.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 4.38
r_work: 0.2838 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8171  Z= 0.112
  Angle     :  0.572   8.825  11053  Z= 0.294
  Chirality :  0.042   0.144   1162
  Planarity :  0.004   0.048   1443
  Dihedral  :  4.582  36.424   1093
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.15 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.36 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  0.12 (0.27), residues: 964
  helix:  3.38 (0.34), residues: 193
  sheet:  0.30 (0.35), residues: 206
  loop : -1.28 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 259 
 TYR   0.013   0.001   TYR D 290 
 PHE   0.012   0.001   PHE D 349 
 TRP   0.037   0.001   TRP D 303 
 HIS   0.003   0.001   HIS D 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 8171)
  covalent geometry    : angle       0.57178 /  0.29 (11053)
  hydrogen bonds       : bond        0.04400 /  2.86 (  332)
  hydrogen bonds       : angle       4.63597 /  3.30 (  960)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 49
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8679 (tm-30)
REVERT: A  464 CYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8168 (p)
REVERT: B  259 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8835 (mp10)
REVERT: B  264 MET cc_start: 0.9299 (tmm) cc_final: 0.9096 (tmm)
REVERT: B  376 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8962 (mmtp)
REVERT: B  404 MET cc_start: 0.9121 (tmm) cc_final: 0.8921 (tmm)
REVERT: D  289 GLN cc_start: 0.9325 (tm-30) cc_final: 0.9123 (tm-30)
REVERT: E  259 ARG cc_start: 0.7522 (mmt180) cc_final: 0.7291 (mmp80)
REVERT: E  325 CYS cc_start: 0.8843 (OUTLIER) cc_final: 0.7953 (t)
  outliers start: 24
  outliers final: 20
  residues processed: 71
  average time/residue: 0.0840
  time to fit residues: 8.7012
Evaluate side-chains
  72 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 48
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  376 LYS
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain D residue  249 ILE
Chi-restraints excluded: chain D residue  301 HIS
Chi-restraints excluded: chain D residue  366 HIS
Chi-restraints excluded: chain D residue  382 VAL
Chi-restraints excluded: chain D residue  413 TYR
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  444 SER
Chi-restraints excluded: chain D residue  470 PHE
Chi-restraints excluded: chain D residue  473 LEU
Chi-restraints excluded: chain E residue  263 GLU
Chi-restraints excluded: chain E residue  325 CYS
Chi-restraints excluded: chain E residue  367 VAL
Chi-restraints excluded: chain E residue  395 THR
Chi-restraints excluded: chain E residue  422 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 19 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.071269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.047515 restraints weight = 37671.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 4.40
r_work: 0.2796 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8171  Z= 0.170
  Angle     :  0.615   8.428  11053  Z= 0.318
  Chirality :  0.043   0.184   1162
  Planarity :  0.004   0.049   1443
  Dihedral  :  4.851  35.955   1093
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.67 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.36 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.01 (0.27), residues: 964
  helix:  3.30 (0.35), residues: 192
  sheet: -0.03 (0.33), residues: 223
  loop : -1.29 (0.25), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 331 
 TYR   0.012   0.001   TYR D 290 
 PHE   0.019   0.002   PHE B 252 
 TRP   0.047   0.002   TRP D 303 
 HIS   0.003   0.001   HIS D 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.17 ( 8171)
  covalent geometry    : angle       0.61456 /  0.32 (11053)
  hydrogen bonds       : bond        0.05164 /  3.38 (  332)
  hydrogen bonds       : angle       4.97723 /  3.56 (  960)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2943.56 seconds
wall clock time: 50 minutes 54.38 seconds (3054.38 seconds total)