Starting phenix.real_space_refine
on Wed Mar  4 00:49:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rra_24657/03_2026/7rra_24657.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rra_24657/03_2026/7rra_24657.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rra_24657/03_2026/7rra_24657.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rra_24657/03_2026/7rra_24657.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rra_24657/03_2026/7rra_24657.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rra_24657/03_2026/7rra_24657.map"
  }
  resolution = 4.4
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6164      2.51       5
     N    1686      2.21       5
     O    1714      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9608
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4804
          Classifications: {'peptide': 602}
          Link IDs: {'PTRANS': 22, 'TRANS': 579}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4804
          Classifications: {'peptide': 602}
          Link IDs: {'PTRANS': 22, 'TRANS': 579}
          Chain breaks: 1
  Time building chain proxies: 2.08, per 1000 atoms: 0.22
  Number of scatterers: 9608
  At special positions: 0
  Unit cell: (112.77, 80.55, 144.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1714      8.00
     N    1686      7.00
     C    6164      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 446.3 milliseconds
  

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2256

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 4 sheets defined
      66.7% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 82
    Processing helix  chain 'A' and resid 89 through 124
    Processing helix  chain 'A' and resid 127 through 174
      removed outlier: 4.565A  pdb=" N   LEU A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
      Proline residue:  A 143  - end of helix
    Processing helix  chain 'A' and resid 179 through 185
    Processing helix  chain 'A' and resid 193 through 236
      removed outlier: 4.260A  pdb=" N   ASP A 200 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
      Proline residue:  A 218  - end of helix
      removed outlier: 4.201A  pdb=" N   ASP A 221 " --> pdb=" O   LYS A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 260
      removed outlier: 5.177A  pdb=" N   LEU A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 288
    Processing helix  chain 'A' and resid 290 through 296
    Processing helix  chain 'A' and resid 299 through 339
      removed outlier: 3.985A  pdb=" N   MET A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LEU A 330 " --> pdb=" O   TRP A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 356
      Proline residue:  A 350  - end of helix
      removed outlier: 4.114A  pdb=" N   THR A 353 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLY A 356 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 370
      removed outlier: 4.799A  pdb=" N   ALA A 364 " --> pdb=" O   ASP A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 442
      removed outlier: 4.841A  pdb=" N   LYS A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   GLU A 408 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   VAL A 409 " --> pdb=" O   SER A 405 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   THR A 410 " --> pdb=" O   TYR A 406 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   GLU A 411 " --> pdb=" O   LYS A 407 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
    Processing helix  chain 'A' and resid 513 through 521
    Processing helix  chain 'A' and resid 553 through 557
    Processing helix  chain 'A' and resid 564 through 568
    Processing helix  chain 'A' and resid 573 through 582
    Processing helix  chain 'A' and resid 586 through 592
    Processing helix  chain 'A' and resid 607 through 621
      removed outlier: 4.148A  pdb=" N   LYS A 610 " --> pdb=" O   GLY A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 650
    Processing helix  chain 'A' and resid 661 through 666
      removed outlier: 3.906A  pdb=" N   TYR A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 82
    Processing helix  chain 'B' and resid 89 through 124
    Processing helix  chain 'B' and resid 127 through 140
    Processing helix  chain 'B' and resid 142 through 175
    Processing helix  chain 'B' and resid 179 through 185
    Processing helix  chain 'B' and resid 193 through 197
    Processing helix  chain 'B' and resid 199 through 236
      Proline residue:  B 218  - end of helix
      removed outlier: 4.202A  pdb=" N   ASP B 221 " --> pdb=" O   LYS B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 260
    Processing helix  chain 'B' and resid 265 through 288
    Processing helix  chain 'B' and resid 290 through 296
    Processing helix  chain 'B' and resid 299 through 355
      removed outlier: 3.908A  pdb=" N   MET B 329 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LEU B 330 " --> pdb=" O   TRP B 326 " (cutoff:3.500A)
      Proline residue:  B 350  - end of helix
      removed outlier: 4.114A  pdb=" N   THR B 353 " --> pdb=" O   VAL B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 370
    Processing helix  chain 'B' and resid 374 through 442
      removed outlier: 4.841A  pdb=" N   LYS B 407 " --> pdb=" O   MET B 403 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   GLU B 408 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   VAL B 409 " --> pdb=" O   SER B 405 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   THR B 410 " --> pdb=" O   TYR B 406 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   GLU B 411 " --> pdb=" O   LYS B 407 " (cutoff:3.500A)
      Proline residue:  B 437  - end of helix
    Processing helix  chain 'B' and resid 513 through 521
    Processing helix  chain 'B' and resid 553 through 557
    Processing helix  chain 'B' and resid 563 through 567
    Processing helix  chain 'B' and resid 573 through 583
    Processing helix  chain 'B' and resid 585 through 592
    Processing helix  chain 'B' and resid 608 through 621
    Processing helix  chain 'B' and resid 637 through 650
    Processing helix  chain 'B' and resid 661 through 666
      removed outlier: 3.906A  pdb=" N   TYR B 666 " --> pdb=" O   SER B 662 " (cutoff:3.500A)
    Processing sheet with id=A, first strand: chain 'A' and resid 466 through 469
      removed outlier: 3.787A  pdb=" N   ILE A 475 " --> pdb=" O   TYR A 532 " (cutoff:3.500A)
    Processing sheet with id=B, first strand: chain 'A' and resid 679 through 683
      removed outlier: 7.458A  pdb=" N   LEU A 654 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 8.547A  pdb=" N   ILE A 505 " --> pdb=" O   LEU A 654 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   SER A 656 " --> pdb=" O   ILE A 505 " (cutoff:3.500A)
      removed outlier: 9.448A  pdb=" N   GLY A 507 " --> pdb=" O   SER A 656 " (cutoff:3.500A)
    Processing sheet with id=C, first strand: chain 'B' and resid 466 through 469
      removed outlier: 3.787A  pdb=" N   ILE B 475 " --> pdb=" O   TYR B 532 " (cutoff:3.500A)
    Processing sheet with id=D, first strand: chain 'B' and resid 503 through 507
      removed outlier: 6.537A  pdb=" N   HIS B 669 " --> pdb=" O   LEU B 504 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   THR B 506 " --> pdb=" O   HIS B 669 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LEU B 671 " --> pdb=" O   THR B 506 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=D

    623 hydrogen bonds defined for protein.
    1746 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: 1.22

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3146
        1.34 -     1.46: 2073
        1.46 -     1.58: 4525
        1.58 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 9818
  Sorted by residual:
  bond pdb=" N   VAL B 183 "
       pdb=" CA  VAL B 183 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.036 1.21e-02 6.83e+03 8.62e+00
  bond pdb=" N   GLU A 498 "
       pdb=" CA  GLU A 498 "
    ideal  model  delta    sigma   weight residual
    1.453  1.490 -0.037 1.31e-02 5.83e+03 8.05e+00
  bond pdb=" N   MET B 539 "
       pdb=" CA  MET B 539 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.21e-02 6.83e+03 7.29e+00
  bond pdb=" N   GLU B 498 "
       pdb=" CA  GLU B 498 "
    ideal  model  delta    sigma   weight residual
    1.453  1.490 -0.037 1.37e-02 5.33e+03 7.25e+00
  bond pdb=" N   MET B 501 "
       pdb=" CA  MET B 501 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.23e-02 6.61e+03 7.14e+00
  ... (remaining 9813 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 12915
        1.56 -     3.11: 308
        3.11 -     4.67: 45
        4.67 -     6.22: 19
        6.22 -     7.78: 7
  Bond angle restraints: 13294
  Sorted by residual:
  angle pdb=" N   GLN A 611 "
        pdb=" CA  GLN A 611 "
        pdb=" C   GLN A 611 "
      ideal   model   delta    sigma   weight residual
     111.71  107.53    4.18 1.15e+00 7.56e-01 1.32e+01
  angle pdb=" N   GLN B 611 "
        pdb=" CA  GLN B 611 "
        pdb=" C   GLN B 611 "
      ideal   model   delta    sigma   weight residual
     111.71  107.57    4.14 1.15e+00 7.56e-01 1.30e+01
  angle pdb=" CA  GLU B 498 "
        pdb=" C   GLU B 498 "
        pdb=" O   GLU B 498 "
      ideal   model   delta    sigma   weight residual
     121.99  118.13    3.86 1.14e+00 7.69e-01 1.14e+01
  angle pdb=" CA  GLN B 472 "
        pdb=" C   GLN B 472 "
        pdb=" O   GLN B 472 "
      ideal   model   delta    sigma   weight residual
     122.03  117.84    4.19 1.25e+00 6.40e-01 1.13e+01
  angle pdb=" CA  GLN A 472 "
        pdb=" C   GLN A 472 "
        pdb=" O   GLN A 472 "
      ideal   model   delta    sigma   weight residual
     122.03  117.86    4.17 1.25e+00 6.40e-01 1.11e+01
  ... (remaining 13289 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.04: 5211
       16.04 -    32.08: 491
       32.08 -    48.12: 159
       48.12 -    64.16: 12
       64.16 -    80.20: 9
  Dihedral angle restraints: 5882
    sinusoidal: 2376
      harmonic: 3506
  Sorted by residual:
  dihedral pdb=" CA  ARG B  69 "
           pdb=" CB  ARG B  69 "
           pdb=" CG  ARG B  69 "
           pdb=" CD  ARG B  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.42   53.42     3      1.50e+01 4.44e-03 9.20e+00
  dihedral pdb=" CA  ARG A  69 "
           pdb=" CB  ARG A  69 "
           pdb=" CG  ARG A  69 "
           pdb=" CD  ARG A  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.37   53.37     3      1.50e+01 4.44e-03 9.20e+00
  dihedral pdb=" CA  TYR B 406 "
           pdb=" C   TYR B 406 "
           pdb=" N   LYS B 407 "
           pdb=" CA  LYS B 407 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -165.18  -14.82     0      5.00e+00 4.00e-02 8.78e+00
  ... (remaining 5879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1191
       0.047 -    0.095: 228
       0.095 -    0.142: 58
       0.142 -    0.190: 5
       0.190 -    0.237: 2
  Chirality restraints: 1484
  Sorted by residual:
  chirality pdb=" CA  LEU B 325 "
            pdb=" N   LEU B 325 "
            pdb=" C   LEU B 325 "
            pdb=" CB  LEU B 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  HIS A 283 "
            pdb=" N   HIS A 283 "
            pdb=" C   HIS A 283 "
            pdb=" CB  HIS A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.62e-01
  chirality pdb=" CA  VAL B 183 "
            pdb=" N   VAL B 183 "
            pdb=" C   VAL B 183 "
            pdb=" CB  VAL B 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.92e-01
  ... (remaining 1481 not shown)

  Planarity restraints: 1688
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 618 "    0.009 2.00e-02 2.50e+03   1.89e-02 3.56e+00
        pdb=" C   MET A 618 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   MET A 618 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE A 619 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 618 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.54e+00
        pdb=" C   MET B 618 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   MET B 618 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE B 619 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 349 "   -0.024 5.00e-02 4.00e+02   3.66e-02 2.15e+00
        pdb=" N   PRO A 350 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 350 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 350 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1685 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2033
        2.79 -     3.32: 10073
        3.32 -     3.84: 15830
        3.84 -     4.37: 17559
        4.37 -     4.90: 29272
  Nonbonded interactions: 74767
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 376 "
            pdb=" OG  SER A 379 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   GLU B 376 "
            pdb=" OG  SER B 379 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OE2 GLU B 272 "
            pdb=" NE2 GLN B 316 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" OE2 GLU A 272 "
            pdb=" NE2 GLN A 316 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" NH2 ARG B 280 "
            pdb=" OE1 GLN A 195 "
     model   vdw
     2.327 3.120
  ... (remaining 74762 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.390
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.280
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5708
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9818  Z= 0.191
  Angle     :  0.593   7.776  13294  Z= 0.338
  Chirality :  0.040   0.237   1484
  Planarity :  0.003   0.037   1688
  Dihedral  : 13.752  80.198   3626
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.24), residues: 1196
  helix:  2.17 (0.18), residues: 816
  sheet:  1.98 (0.48), residues: 88
  loop : -1.51 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 538 
 TYR   0.020   0.001   TYR A 171 
 PHE   0.007   0.001   PHE A 385 
 TRP   0.011   0.001   TRP A 601 
 HIS   0.003   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9818)
  covalent geometry    : angle       0.59314 (13294)
  hydrogen bonds       : bond        0.05341 (  623)
  hydrogen bonds       : angle       4.38832 ( 1746)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  428 ASP cc_start: 0.7080 (t0) cc_final: 0.6571 (t70)
REVERT: B  501 MET cc_start: 0.5014 (ppp) cc_final: 0.3872 (ppp)
REVERT: A  428 ASP cc_start: 0.7418 (t0) cc_final: 0.7052 (t0)
REVERT: A  501 MET cc_start: 0.6363 (ppp) cc_final: 0.5200 (ppp)
REVERT: A  674 ASP cc_start: 0.6859 (p0) cc_final: 0.6443 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1290
  time to fit residues: 17.5347
Evaluate side-chains
  72 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    8.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 611 GLN
** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.097565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.087861 restraints weight = 71683.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.089676 restraints weight = 43456.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.090928 restraints weight = 29513.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.091714 restraints weight = 21777.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.092198 restraints weight = 17503.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5986
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9818  Z= 0.143
  Angle     :  0.549   8.244  13294  Z= 0.286
  Chirality :  0.038   0.150   1484
  Planarity :  0.004   0.031   1688
  Dihedral  :  3.930  16.234   1344
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.24), residues: 1196
  helix:  2.07 (0.18), residues: 808
  sheet:  1.94 (0.46), residues: 88
  loop : -1.45 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 172 
 TYR   0.022   0.001   TYR B 171 
 PHE   0.008   0.001   PHE B  71 
 TRP   0.009   0.001   TRP A 339 
 HIS   0.004   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9818)
  covalent geometry    : angle       0.54887 (13294)
  hydrogen bonds       : bond        0.04630 (  623)
  hydrogen bonds       : angle       4.18233 ( 1746)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  155 GLU cc_start: 0.7310 (tm-30) cc_final: 0.7095 (mt-10)
REVERT: B  428 ASP cc_start: 0.8106 (t0) cc_final: 0.7456 (t70)
REVERT: B  501 MET cc_start: 0.5463 (ppp) cc_final: 0.4393 (ppp)
REVERT: B  539 MET cc_start: 0.8748 (mpp) cc_final: 0.8515 (mpp)
REVERT: A  130 PHE cc_start: 0.7228 (m-10) cc_final: 0.6464 (m-10)
REVERT: A  146 PHE cc_start: 0.8031 (t80) cc_final: 0.6779 (t80)
REVERT: A  155 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7196 (mt-10)
REVERT: A  428 ASP cc_start: 0.7850 (t0) cc_final: 0.7418 (t0)
REVERT: A  501 MET cc_start: 0.6406 (ppp) cc_final: 0.5607 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1154
  time to fit residues: 14.9992
Evaluate side-chains
  71 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 108 optimal weight:    4.9990
   chunk 41 optimal weight:   20.0000
   chunk 119 optimal weight:    8.9990
   chunk 76 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 92 optimal weight:   10.0000
   chunk 95 optimal weight:    5.9990
   chunk 111 optimal weight:    0.0170
   chunk 64 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    4.6026

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

Flipped N/Q/H residues before XYZ refinement:
B 289 ASN
B 299 HIS
** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 HIS
** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.090607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.080991 restraints weight = 73505.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.082625 restraints weight = 45183.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.083759 restraints weight = 30906.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.084525 restraints weight = 22993.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.084938 restraints weight = 18361.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6268
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9818  Z= 0.246
  Angle     :  0.749   7.786  13294  Z= 0.399
  Chirality :  0.046   0.207   1484
  Planarity :  0.006   0.056   1688
  Dihedral  :  4.705  21.850   1344
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 20.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  6.31 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.48 (0.23), residues: 1196
  helix:  0.90 (0.17), residues: 812
  sheet:  1.36 (0.46), residues: 92
  loop : -1.58 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 259 
 TYR   0.038   0.002   TYR B 171 
 PHE   0.025   0.003   PHE A 175 
 TRP   0.017   0.002   TRP A 339 
 HIS   0.006   0.002   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 9818)
  covalent geometry    : angle       0.74900 (13294)
  hydrogen bonds       : bond        0.06542 (  623)
  hydrogen bonds       : angle       5.13043 ( 1746)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: B  186 MET cc_start: 0.6788 (tmm) cc_final: 0.6414 (tmm)
REVERT: B  428 ASP cc_start: 0.8041 (t0) cc_final: 0.7400 (t70)
REVERT: B  501 MET cc_start: 0.6497 (ppp) cc_final: 0.5300 (ppp)
REVERT: A  146 PHE cc_start: 0.7991 (t80) cc_final: 0.6942 (t80)
REVERT: A  186 MET cc_start: 0.6419 (tmm) cc_final: 0.5948 (tmm)
REVERT: A  428 ASP cc_start: 0.8151 (t0) cc_final: 0.7780 (t70)
REVERT: A  501 MET cc_start: 0.6503 (ppp) cc_final: 0.5497 (ppp)
  outliers start: 1
  outliers final: 1
  residues processed: 88
  average time/residue: 0.1219
  time to fit residues: 14.3548
Evaluate side-chains
  70 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 44 optimal weight:   20.0000
   chunk 33 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 502 HIS
A 502 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.092966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.083155 restraints weight = 73109.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.084924 restraints weight = 44307.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.086133 restraints weight = 30186.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.086931 restraints weight = 22360.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.087496 restraints weight = 17795.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6182
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9818  Z= 0.155
  Angle     :  0.592  10.816  13294  Z= 0.312
  Chirality :  0.040   0.173   1484
  Planarity :  0.005   0.060   1688
  Dihedral  :  4.405  20.625   1344
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.24), residues: 1196
  helix:  1.44 (0.17), residues: 810
  sheet:  1.36 (0.47), residues: 88
  loop : -1.58 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 152 
 TYR   0.037   0.002   TYR B 171 
 PHE   0.015   0.002   PHE A 175 
 TRP   0.011   0.001   TRP A  77 
 HIS   0.006   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9818)
  covalent geometry    : angle       0.59228 (13294)
  hydrogen bonds       : bond        0.05845 (  623)
  hydrogen bonds       : angle       4.73569 ( 1746)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 ARG cc_start: 0.7230 (mmp-170) cc_final: 0.7000 (mmp80)
REVERT: B  186 MET cc_start: 0.6832 (tmm) cc_final: 0.6520 (tmm)
REVERT: B  325 LEU cc_start: 0.7625 (mp) cc_final: 0.7240 (mp)
REVERT: B  428 ASP cc_start: 0.8363 (t0) cc_final: 0.7764 (t70)
REVERT: B  501 MET cc_start: 0.6518 (ppp) cc_final: 0.5496 (ppp)
REVERT: B  539 MET cc_start: 0.9066 (mpp) cc_final: 0.8864 (mpp)
REVERT: A  146 PHE cc_start: 0.7892 (t80) cc_final: 0.6775 (t80)
REVERT: A  186 MET cc_start: 0.6358 (tmm) cc_final: 0.5906 (tmm)
REVERT: A  428 ASP cc_start: 0.7875 (t0) cc_final: 0.7560 (t70)
REVERT: A  501 MET cc_start: 0.6525 (ppp) cc_final: 0.5437 (ppp)
REVERT: A  516 LEU cc_start: 0.8448 (tp) cc_final: 0.8073 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1026
  time to fit residues: 12.6290
Evaluate side-chains
  75 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 100 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 50 optimal weight:    0.0870
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 55 optimal weight:    9.9990
   chunk 119 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    3.2166

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.091210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.081603 restraints weight = 73330.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.083318 restraints weight = 44767.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.084480 restraints weight = 30372.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.085263 restraints weight = 22544.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.085724 restraints weight = 17923.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6252
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9818  Z= 0.188
  Angle     :  0.637   9.073  13294  Z= 0.341
  Chirality :  0.041   0.177   1484
  Planarity :  0.005   0.047   1688
  Dihedral  :  4.566  20.995   1344
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.23), residues: 1196
  helix:  1.19 (0.17), residues: 808
  sheet:  1.32 (0.49), residues: 88
  loop : -1.65 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 120 
 TYR   0.039   0.002   TYR A 171 
 PHE   0.022   0.002   PHE A 175 
 TRP   0.014   0.001   TRP B  77 
 HIS   0.006   0.002   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 9818)
  covalent geometry    : angle       0.63705 (13294)
  hydrogen bonds       : bond        0.06153 (  623)
  hydrogen bonds       : angle       4.87032 ( 1746)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 ARG cc_start: 0.7385 (mmp-170) cc_final: 0.6987 (mmp80)
REVERT: B  186 MET cc_start: 0.6877 (tmm) cc_final: 0.6594 (tmm)
REVERT: B  325 LEU cc_start: 0.7675 (mp) cc_final: 0.7327 (mp)
REVERT: B  428 ASP cc_start: 0.8389 (t0) cc_final: 0.7833 (t70)
REVERT: B  501 MET cc_start: 0.7042 (ppp) cc_final: 0.5985 (ppp)
REVERT: B  539 MET cc_start: 0.9002 (mpp) cc_final: 0.8720 (mpp)
REVERT: A  146 PHE cc_start: 0.8009 (t80) cc_final: 0.6953 (t80)
REVERT: A  186 MET cc_start: 0.6435 (tmm) cc_final: 0.6049 (tmm)
REVERT: A  428 ASP cc_start: 0.8227 (t0) cc_final: 0.7909 (t0)
REVERT: A  501 MET cc_start: 0.6393 (ppp) cc_final: 0.5909 (ppp)
REVERT: A  516 LEU cc_start: 0.8386 (tp) cc_final: 0.8021 (pp)
REVERT: A  539 MET cc_start: 0.8413 (mpp) cc_final: 0.7651 (mpp)
REVERT: A  548 MET cc_start: 0.3080 (ppp) cc_final: 0.2842 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1152
  time to fit residues: 14.5249
Evaluate side-chains
  77 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 83 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 94 optimal weight:    6.9990
   chunk 118 optimal weight:    7.9990
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 114 optimal weight:    0.0970
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4257 r_free = 0.4257 target = 0.093662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.083457 restraints weight = 71800.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.085341 restraints weight = 43649.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.086588 restraints weight = 29638.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.087481 restraints weight = 21891.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.088000 restraints weight = 17274.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6146
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9818  Z= 0.135
  Angle     :  0.580  10.895  13294  Z= 0.300
  Chirality :  0.039   0.192   1484
  Planarity :  0.004   0.043   1688
  Dihedral  :  4.371  20.922   1344
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.24), residues: 1196
  helix:  1.68 (0.17), residues: 802
  sheet:  1.35 (0.50), residues: 88
  loop : -1.50 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 401 
 TYR   0.028   0.002   TYR A 171 
 PHE   0.022   0.001   PHE A 130 
 TRP   0.009   0.001   TRP A 339 
 HIS   0.005   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9818)
  covalent geometry    : angle       0.58013 (13294)
  hydrogen bonds       : bond        0.05605 (  623)
  hydrogen bonds       : angle       4.55059 ( 1746)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 ARG cc_start: 0.7126 (mmp-170) cc_final: 0.6824 (mmp80)
REVERT: B  186 MET cc_start: 0.6897 (tmm) cc_final: 0.6549 (tmm)
REVERT: B  357 TYR cc_start: 0.6891 (m-10) cc_final: 0.6689 (m-10)
REVERT: B  428 ASP cc_start: 0.8105 (t0) cc_final: 0.7633 (t70)
REVERT: B  501 MET cc_start: 0.6677 (ppp) cc_final: 0.5695 (ppp)
REVERT: B  539 MET cc_start: 0.8963 (mpp) cc_final: 0.8711 (mpp)
REVERT: B  602 LYS cc_start: 0.6573 (mmtt) cc_final: 0.6305 (mmmt)
REVERT: A  146 PHE cc_start: 0.7896 (t80) cc_final: 0.6752 (t80)
REVERT: A  172 ARG cc_start: 0.5652 (mmp-170) cc_final: 0.5423 (mmp-170)
REVERT: A  186 MET cc_start: 0.6429 (tmm) cc_final: 0.5969 (tmm)
REVERT: A  428 ASP cc_start: 0.8100 (t0) cc_final: 0.7814 (t0)
REVERT: A  501 MET cc_start: 0.6576 (ppp) cc_final: 0.5927 (ppp)
REVERT: A  516 LEU cc_start: 0.8443 (tp) cc_final: 0.8098 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1116
  time to fit residues: 14.5993
Evaluate side-chains
  78 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 108 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 110 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 104 optimal weight:   20.0000
   chunk 42 optimal weight:   30.0000
   chunk 71 optimal weight:    3.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.088647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.079217 restraints weight = 73636.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.080874 restraints weight = 44992.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.081990 restraints weight = 30765.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.082729 restraints weight = 22911.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.083189 restraints weight = 18317.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6326
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9818  Z= 0.233
  Angle     :  0.750  13.405  13294  Z= 0.402
  Chirality :  0.045   0.301   1484
  Planarity :  0.006   0.048   1688
  Dihedral  :  4.887  21.370   1344
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 21.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.23), residues: 1196
  helix:  0.79 (0.17), residues: 810
  sheet:  0.98 (0.51), residues: 88
  loop : -1.89 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 120 
 TYR   0.043   0.003   TYR A 171 
 PHE   0.024   0.003   PHE A 175 
 TRP   0.020   0.002   TRP B  77 
 HIS   0.008   0.002   HIS B 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 9818)
  covalent geometry    : angle       0.75048 (13294)
  hydrogen bonds       : bond        0.06869 (  623)
  hydrogen bonds       : angle       5.25082 ( 1746)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.388 
Fit side-chains
REVERT: B  130 PHE cc_start: 0.7246 (m-80) cc_final: 0.6830 (m-80)
REVERT: B  155 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7237 (mt-10)
REVERT: B  186 MET cc_start: 0.6829 (tmm) cc_final: 0.6340 (tmm)
REVERT: B  357 TYR cc_start: 0.6584 (m-10) cc_final: 0.6296 (m-10)
REVERT: B  428 ASP cc_start: 0.8009 (t0) cc_final: 0.7440 (t70)
REVERT: B  501 MET cc_start: 0.6466 (ppp) cc_final: 0.5932 (ppp)
REVERT: B  539 MET cc_start: 0.9071 (mpp) cc_final: 0.8743 (mpp)
REVERT: A  122 ILE cc_start: 0.7609 (mt) cc_final: 0.7380 (mt)
REVERT: A  186 MET cc_start: 0.6542 (tmm) cc_final: 0.6058 (tmm)
REVERT: A  257 VAL cc_start: 0.9174 (t) cc_final: 0.8948 (m)
REVERT: A  428 ASP cc_start: 0.8249 (t0) cc_final: 0.7931 (t0)
REVERT: A  501 MET cc_start: 0.5947 (ppp) cc_final: 0.5578 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0954
  time to fit residues: 11.5752
Evaluate side-chains
  73 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 99 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 72 optimal weight:   20.0000
   chunk 100 optimal weight:    0.0570
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    3.2106

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

Flipped N/Q/H residues before XYZ refinement:
B 586 HIS
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.089802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.080478 restraints weight = 73768.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.082183 restraints weight = 44947.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.083330 restraints weight = 30348.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.084075 restraints weight = 22553.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.084618 restraints weight = 17973.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6266
moved from start:          0.4259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9818  Z= 0.188
  Angle     :  0.665  12.286  13294  Z= 0.354
  Chirality :  0.042   0.224   1484
  Planarity :  0.004   0.045   1688
  Dihedral  :  4.741  22.216   1344
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 18.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.23), residues: 1196
  helix:  0.98 (0.17), residues: 810
  sheet:  0.81 (0.51), residues: 88
  loop : -1.85 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 172 
 TYR   0.039   0.002   TYR A 171 
 PHE   0.018   0.002   PHE A 175 
 TRP   0.022   0.002   TRP B  77 
 HIS   0.005   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9818)
  covalent geometry    : angle       0.66517 (13294)
  hydrogen bonds       : bond        0.06545 (  623)
  hydrogen bonds       : angle       5.02884 ( 1746)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.472 
Fit side-chains
REVERT: B  146 PHE cc_start: 0.7779 (t80) cc_final: 0.6685 (t80)
REVERT: B  152 ARG cc_start: 0.8384 (tmm-80) cc_final: 0.8027 (ttt180)
REVERT: B  155 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7199 (mt-10)
REVERT: B  186 MET cc_start: 0.6987 (tmm) cc_final: 0.6580 (tmm)
REVERT: B  325 LEU cc_start: 0.7531 (mp) cc_final: 0.7266 (mp)
REVERT: B  357 TYR cc_start: 0.6507 (m-10) cc_final: 0.6219 (m-10)
REVERT: B  428 ASP cc_start: 0.8215 (t0) cc_final: 0.7722 (t70)
REVERT: B  501 MET cc_start: 0.6292 (ppp) cc_final: 0.5888 (ppp)
REVERT: B  539 MET cc_start: 0.9057 (mpp) cc_final: 0.8795 (mpp)
REVERT: A  146 PHE cc_start: 0.8061 (t80) cc_final: 0.7007 (t80)
REVERT: A  186 MET cc_start: 0.6375 (tmm) cc_final: 0.5851 (tmm)
REVERT: A  428 ASP cc_start: 0.8171 (t0) cc_final: 0.7860 (t0)
REVERT: A  501 MET cc_start: 0.5759 (ppp) cc_final: 0.5541 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0996
  time to fit residues: 11.8523
Evaluate side-chains
  75 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   chunk 114 optimal weight:    0.0470
   chunk 115 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0570
   chunk 68 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.0200

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

Flipped N/Q/H residues before XYZ refinement:
B 210 HIS
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.092638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.083289 restraints weight = 72400.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.085086 restraints weight = 43879.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.086216 restraints weight = 29550.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.087031 restraints weight = 21886.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.087512 restraints weight = 17275.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6162
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9818  Z= 0.142
  Angle     :  0.605  12.059  13294  Z= 0.316
  Chirality :  0.041   0.168   1484
  Planarity :  0.004   0.042   1688
  Dihedral  :  4.520  22.092   1344
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.24), residues: 1196
  helix:  1.44 (0.17), residues: 818
  sheet:  0.75 (0.52), residues: 88
  loop : -1.61 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 401 
 TYR   0.028   0.002   TYR A 171 
 PHE   0.014   0.001   PHE A  83 
 TRP   0.015   0.001   TRP B  77 
 HIS   0.005   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9818)
  covalent geometry    : angle       0.60496 (13294)
  hydrogen bonds       : bond        0.05837 (  623)
  hydrogen bonds       : angle       4.58911 ( 1746)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: B  146 PHE cc_start: 0.7830 (t80) cc_final: 0.6798 (t80)
REVERT: B  186 MET cc_start: 0.6542 (tmm) cc_final: 0.5893 (tmm)
REVERT: B  346 MET cc_start: 0.7865 (mmp) cc_final: 0.7450 (mmp)
REVERT: B  357 TYR cc_start: 0.6537 (m-10) cc_final: 0.6229 (m-10)
REVERT: B  422 MET cc_start: 0.6179 (tmm) cc_final: 0.5957 (tmm)
REVERT: B  428 ASP cc_start: 0.7994 (t0) cc_final: 0.7534 (t0)
REVERT: B  501 MET cc_start: 0.5967 (ppp) cc_final: 0.5470 (ppp)
REVERT: B  539 MET cc_start: 0.8997 (mpp) cc_final: 0.8779 (mpp)
REVERT: A  146 PHE cc_start: 0.8049 (t80) cc_final: 0.7074 (t80)
REVERT: A  186 MET cc_start: 0.6300 (tmm) cc_final: 0.5755 (tmm)
REVERT: A  428 ASP cc_start: 0.8038 (t0) cc_final: 0.7740 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0948
  time to fit residues: 12.5467
Evaluate side-chains
  76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:   20.0000
   chunk 48 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN
B 307 GLN
** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.088263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.078999 restraints weight = 74181.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.080661 restraints weight = 44977.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.081806 restraints weight = 30531.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.082564 restraints weight = 22606.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.083000 restraints weight = 17962.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6305
moved from start:          0.4610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9818  Z= 0.227
  Angle     :  0.754  15.213  13294  Z= 0.401
  Chirality :  0.045   0.318   1484
  Planarity :  0.006   0.045   1688
  Dihedral  :  5.012  23.396   1344
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 21.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.23), residues: 1196
  helix:  0.74 (0.17), residues: 808
  sheet:  0.46 (0.53), residues: 88
  loop : -1.93 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 259 
 TYR   0.037   0.002   TYR A 171 
 PHE   0.023   0.003   PHE A 175 
 TRP   0.029   0.002   TRP B 595 
 HIS   0.008   0.002   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 9818)
  covalent geometry    : angle       0.75450 (13294)
  hydrogen bonds       : bond        0.06795 (  623)
  hydrogen bonds       : angle       5.23303 ( 1746)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.360 
Fit side-chains
REVERT: B  146 PHE cc_start: 0.8063 (t80) cc_final: 0.6788 (t80)
REVERT: B  186 MET cc_start: 0.6612 (tmm) cc_final: 0.6092 (tmm)
REVERT: B  357 TYR cc_start: 0.6560 (m-10) cc_final: 0.6228 (m-10)
REVERT: B  428 ASP cc_start: 0.8353 (t0) cc_final: 0.7924 (t70)
REVERT: B  501 MET cc_start: 0.5699 (ppp) cc_final: 0.5473 (ppp)
REVERT: A  186 MET cc_start: 0.6401 (tmm) cc_final: 0.5860 (tmm)
REVERT: A  257 VAL cc_start: 0.9196 (t) cc_final: 0.8964 (m)
REVERT: A  428 ASP cc_start: 0.8155 (t0) cc_final: 0.7870 (t0)
REVERT: A  501 MET cc_start: 0.5502 (ppp) cc_final: 0.5120 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0993
  time to fit residues: 11.7516
Evaluate side-chains
  74 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 105 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 119 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9990
   chunk 102 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.092262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.082819 restraints weight = 72199.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.084629 restraints weight = 43759.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.085819 restraints weight = 29598.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.086617 restraints weight = 21839.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.087091 restraints weight = 17275.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6180
moved from start:          0.4273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9818  Z= 0.151
  Angle     :  0.630  14.724  13294  Z= 0.326
  Chirality :  0.041   0.208   1484
  Planarity :  0.004   0.044   1688
  Dihedral  :  4.633  22.941   1344
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.24), residues: 1196
  helix:  1.30 (0.17), residues: 816
  sheet:  0.45 (0.53), residues: 88
  loop : -1.64 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 104 
 TYR   0.029   0.002   TYR A 171 
 PHE   0.013   0.002   PHE A  83 
 TRP   0.017   0.001   TRP B  77 
 HIS   0.003   0.001   HIS B 584 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9818)
  covalent geometry    : angle       0.62976 (13294)
  hydrogen bonds       : bond        0.05904 (  623)
  hydrogen bonds       : angle       4.69617 ( 1746)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1420.70 seconds
wall clock time: 25 minutes 22.89 seconds (1522.89 seconds total)