Starting phenix.real_space_refine
on Tue Mar  3 11:25:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x2z_22014/03_2026/6x2z_22014.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x2z_22014/03_2026/6x2z_22014.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x2z_22014/03_2026/6x2z_22014.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x2z_22014/03_2026/6x2z_22014.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x2z_22014/03_2026/6x2z_22014.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x2z_22014/03_2026/6x2z_22014.map"
  }
  resolution = 3.03
  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=   0.003
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
     S      23      5.16       5
     Na      3      4.78       5
     C    2094      2.51       5
     N     511      2.21       5
     O     574      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s

  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: 3205
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3202
          Classifications: {'peptide': 420}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 408}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' NA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 0.80, per 1000 atoms: 0.25
  Number of scatterers: 3205
  At special positions: 0
  Unit cell: (67.392, 67.392, 82.368, 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      23     16.00
     Na      3     11.00
     O     574      8.00
     N     511      7.00
     C    2094      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: 0.26
  Conformation dependent library (CDL) restraints added in 139.2 milliseconds
  

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  776

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 1 sheets defined
      79.3% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 42
      removed outlier: 3.778A  pdb=" N   LEU A  22 " --> pdb=" O   ASN A  18 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   THR A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A  37 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   ARG A  39 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLU A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 53 through 81
      removed outlier: 3.798A  pdb=" N   ILE A  66 " --> pdb=" O   MET A  62 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LEU A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      Proline residue:  A  69  - end of helix
      removed outlier: 3.887A  pdb=" N   VAL A  79 " --> pdb=" O   MET A  75 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 117
      removed outlier: 3.525A  pdb=" N   LEU A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TYR A  97 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   ILE A 104 " --> pdb=" O   CYS A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 150
      removed outlier: 3.694A  pdb=" N   ASP A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ILE A 146 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   PHE A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 158
      removed outlier: 3.572A  pdb=" N   CYS A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 228
    Processing helix  chain 'A' and resid 229 through 232
      removed outlier: 3.621A  pdb=" N   LYS A 232 " --> pdb=" O   MET A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 229 through 232'
    Processing helix  chain 'A' and resid 233 through 250
      removed outlier: 3.584A  pdb=" N   MET A 248 " --> pdb=" O   SER A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 266
      removed outlier: 4.092A  pdb=" N   CYS A 256 " --> pdb=" O   GLN A 252 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      Proline residue:  A 259  - end of helix
      removed outlier: 3.894A  pdb=" N   PHE A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 280
      removed outlier: 4.679A  pdb=" N   ILE A 278 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE A 279 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 299
      removed outlier: 4.204A  pdb=" N   THR A 291 " --> pdb=" O   ALA A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 309
      removed outlier: 3.503A  pdb=" N   TYR A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE A 306 " --> pdb=" O   PRO A 302 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL A 308 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 320
      removed outlier: 3.725A  pdb=" N   PHE A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 331
      removed outlier: 3.560A  pdb=" N   MET A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 346
    Processing helix  chain 'A' and resid 351 through 365
      removed outlier: 3.555A  pdb=" N   ARG A 356 " --> pdb=" O   LYS A 352 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   PHE A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      Proline residue:  A 360  - end of helix
      removed outlier: 3.889A  pdb=" N   THR A 364 " --> pdb=" O   PRO A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 384
      removed outlier: 4.054A  pdb=" N   VAL A 379 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 408
      removed outlier: 3.871A  pdb=" N   ILE A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   THR A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR A 402 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
      removed outlier: 3.714A  pdb=" N   VAL A 422 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL A 426 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 436
      removed outlier: 3.519A  pdb=" N   ASP A 432 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   THR A 434 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LEU A 435 " --> pdb=" O   ASP A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 466
      removed outlier: 3.674A  pdb=" N   PHE A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET A 449 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A 450 " --> pdb=" O   PHE A 446 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN A 451 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 471
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167

    192 hydrogen bonds defined for protein.
    567 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: 0.33

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 638
        1.33 -     1.45: 651
        1.45 -     1.57: 1917
        1.57 -     1.69: 0
        1.69 -     1.81: 41
  Bond restraints: 3247
  Sorted by residual:
  bond pdb=" N   GLN A 122 "
       pdb=" CA  GLN A 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 9.00e-03 1.23e+04 8.97e+00
  bond pdb=" N   VAL A 124 "
       pdb=" CA  VAL A 124 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.032 1.19e-02 7.06e+03 7.10e+00
  bond pdb=" C   ASN A 451 "
       pdb=" O   ASN A 451 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.027 1.17e-02 7.31e+03 5.23e+00
  bond pdb=" N   VAL A 450 "
       pdb=" CA  VAL A 450 "
    ideal  model  delta    sigma   weight residual
    1.460  1.433  0.026 1.21e-02 6.83e+03 4.73e+00
  bond pdb=" C   LEU A 453 "
       pdb=" O   LEU A 453 "
    ideal  model  delta    sigma   weight residual
    1.237  1.211  0.025 1.17e-02 7.31e+03 4.67e+00
  ... (remaining 3242 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 4201
        1.72 -     3.44: 164
        3.44 -     5.15: 26
        5.15 -     6.87: 7
        6.87 -     8.59: 5
  Bond angle restraints: 4403
  Sorted by residual:
  angle pdb=" N   ALA A 414 "
        pdb=" CA  ALA A 414 "
        pdb=" C   ALA A 414 "
      ideal   model   delta    sigma   weight residual
     113.16  104.57    8.59 1.24e+00 6.50e-01 4.80e+01
  angle pdb=" C   GLY A 283 "
        pdb=" N   LEU A 284 "
        pdb=" CA  LEU A 284 "
      ideal   model   delta    sigma   weight residual
     121.54  129.00   -7.46 1.91e+00 2.74e-01 1.53e+01
  angle pdb=" N   ILE A 271 "
        pdb=" CA  ILE A 271 "
        pdb=" C   ILE A 271 "
      ideal   model   delta    sigma   weight residual
     112.29  108.77    3.52 9.40e-01 1.13e+00 1.40e+01
  angle pdb=" N   GLN A 122 "
        pdb=" CA  GLN A 122 "
        pdb=" C   GLN A 122 "
      ideal   model   delta    sigma   weight residual
     113.50  107.77    5.73 1.65e+00 3.67e-01 1.21e+01
  angle pdb=" C   THR A 121 "
        pdb=" N   GLN A 122 "
        pdb=" CA  GLN A 122 "
      ideal   model   delta    sigma   weight residual
     120.17  125.31   -5.14 1.54e+00 4.22e-01 1.11e+01
  ... (remaining 4398 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.57: 1671
       15.57 -    31.13: 198
       31.13 -    46.69: 58
       46.69 -    62.25: 12
       62.25 -    77.82: 7
  Dihedral angle restraints: 1946
    sinusoidal: 744
      harmonic: 1202
  Sorted by residual:
  dihedral pdb=" CA  GLU A 272 "
           pdb=" C   GLU A 272 "
           pdb=" N   VAL A 273 "
           pdb=" CA  VAL A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.92  -22.08     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  THR A 247 "
           pdb=" C   THR A 247 "
           pdb=" N   MET A 248 "
           pdb=" CA  MET A 248 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.07   17.93     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ASP A  83 "
           pdb=" C   ASP A  83 "
           pdb=" N   SER A  84 "
           pdb=" CA  SER A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.15   16.85     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 1943 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 468
       0.067 -    0.135: 79
       0.135 -    0.202: 7
       0.202 -    0.269: 3
       0.269 -    0.336: 1
  Chirality restraints: 558
  Sorted by residual:
  chirality pdb=" CA  ASP A 440 "
            pdb=" N   ASP A 440 "
            pdb=" C   ASP A 440 "
            pdb=" CB  ASP A 440 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" CA  GLN A 413 "
            pdb=" N   GLN A 413 "
            pdb=" C   GLN A 413 "
            pdb=" CB  GLN A 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  ASP A 368 "
            pdb=" N   ASP A 368 "
            pdb=" C   ASP A 368 "
            pdb=" CB  ASP A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 555 not shown)

  Planarity restraints: 537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 301 "   -0.041 5.00e-02 4.00e+02   6.17e-02 6.08e+00
        pdb=" N   PRO A 302 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 302 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 302 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 121 "    0.012 2.00e-02 2.50e+03   2.42e-02 5.84e+00
        pdb=" C   THR A 121 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   THR A 121 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLN A 122 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 337 "    0.037 5.00e-02 4.00e+02   5.51e-02 4.85e+00
        pdb=" N   PRO A 338 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 338 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 338 "    0.031 5.00e-02 4.00e+02
  ... (remaining 534 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 78
        2.69 -     3.24: 3006
        3.24 -     3.79: 4910
        3.79 -     4.35: 6687
        4.35 -     4.90: 10760
  Nonbonded interactions: 25441
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 366 "
            pdb="NA    NA A 601 "
     model   vdw
     2.131 2.470
  nonbonded pdb=" O   LYS A  16 "
            pdb=" OD1 ASN A  17 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG1 THR A 102 "
            pdb="NA    NA A 603 "
     model   vdw
     2.242 2.470
  nonbonded pdb=" O   ASP A 444 "
            pdb=" OG1 THR A 448 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG1 THR A 370 "
            pdb=" OD2 ASP A 600 "
     model   vdw
     2.318 3.040
  ... (remaining 25436 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.900
  Find NCS groups from input model:        0.010
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
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      :  0.005   0.040   3247  Z= 0.267
  Angle     :  0.835   8.589   4403  Z= 0.502
  Chirality :  0.054   0.336    558
  Planarity :  0.006   0.062    537
  Dihedral  : 15.506  77.817   1170
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.68 %
    Favored  : 79.32 %
  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: -5.65 (0.28), residues: 413
  helix: -4.09 (0.16), residues: 296
  sheet: -1.37 (1.46), residues: 18
  loop : -1.95 (0.52), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 447 
 TYR   0.011   0.001   TYR A 257 
 PHE   0.011   0.001   PHE A 159 
 TRP   0.003   0.001   TRP A  19 
 HIS   0.001   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 3247)
  covalent geometry    : angle       0.83516 ( 4403)
  hydrogen bonds       : bond        0.32748 (  192)
  hydrogen bonds       : angle      10.94008 (  567)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  255 MET cc_start: 0.8605 (tpp) cc_final: 0.8162 (mmp)
REVERT: A  352 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7944 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0432
  time to fit residues: 3.9424
Evaluate side-chains
  55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 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 = 0.3804 r_free = 0.3804 target = 0.143424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.108152 restraints weight = 4731.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.22
r_work: 0.3117 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3247  Z= 0.127
  Angle     :  0.585   7.516   4403  Z= 0.311
  Chirality :  0.040   0.134    558
  Planarity :  0.005   0.042    537
  Dihedral  :  5.191  20.704    440
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 21.25 %
    Favored  : 76.77 %
  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: -3.04 (0.36), residues: 413
  helix: -1.88 (0.25), residues: 307
  sheet: -0.70 (1.46), residues: 18
  loop : -1.91 (0.59), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  39 
 TYR   0.008   0.001   TYR A  51 
 PHE   0.012   0.001   PHE A 218 
 TRP   0.008   0.001   TRP A 276 
 HIS   0.009   0.003   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 3247)
  covalent geometry    : angle       0.58472 ( 4403)
  hydrogen bonds       : bond        0.04478 (  192)
  hydrogen bonds       : angle       5.11652 (  567)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A  205 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8213 (pmm)
REVERT: A  255 MET cc_start: 0.9179 (tpp) cc_final: 0.8679 (mmp)
REVERT: A  277 GLU cc_start: 0.8610 (tp30) cc_final: 0.8325 (tp30)
REVERT: A  455 ASP cc_start: 0.8379 (m-30) cc_final: 0.7944 (m-30)
  outliers start: 7
  outliers final: 1
  residues processed: 65
  average time/residue: 0.0324
  time to fit residues: 3.0878
Evaluate side-chains
  52 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  426 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 7 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0870
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 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 = 0.3774 r_free = 0.3774 target = 0.142044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.105170 restraints weight = 4728.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.28
r_work: 0.3126 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3247  Z= 0.109
  Angle     :  0.525   5.602   4403  Z= 0.276
  Chirality :  0.040   0.153    558
  Planarity :  0.004   0.034    537
  Dihedral  :  4.739  17.003    440
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 24.08 %
    Favored  : 74.22 %
  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: -1.40 (0.41), residues: 413
  helix: -0.57 (0.30), residues: 307
  sheet: -0.39 (1.45), residues: 18
  loop : -1.75 (0.60), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  39 
 TYR   0.006   0.001   TYR A 257 
 PHE   0.011   0.001   PHE A 218 
 TRP   0.007   0.001   TRP A 276 
 HIS   0.006   0.002   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 3247)
  covalent geometry    : angle       0.52527 ( 4403)
  hydrogen bonds       : bond        0.03517 (  192)
  hydrogen bonds       : angle       4.42614 (  567)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A  205 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8215 (pmm)
REVERT: A  255 MET cc_start: 0.9037 (tpp) cc_final: 0.8500 (mmp)
REVERT: A  455 ASP cc_start: 0.8229 (m-30) cc_final: 0.7839 (m-30)
  outliers start: 6
  outliers final: 4
  residues processed: 63
  average time/residue: 0.0259
  time to fit residues: 2.4153
Evaluate side-chains
  60 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  426 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 10 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 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 = 0.3741 r_free = 0.3741 target = 0.139322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.101690 restraints weight = 4683.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.29
r_work: 0.3095 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3247  Z= 0.139
  Angle     :  0.529   5.581   4403  Z= 0.277
  Chirality :  0.041   0.162    558
  Planarity :  0.004   0.030    537
  Dihedral  :  4.591  17.201    440
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 24.08 %
    Favored  : 72.52 %
  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: -0.79 (0.42), residues: 413
  helix: -0.10 (0.31), residues: 308
  sheet: -0.24 (1.46), residues: 18
  loop : -1.66 (0.62), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  93 
 TYR   0.006   0.001   TYR A 305 
 PHE   0.012   0.001   PHE A 218 
 TRP   0.006   0.001   TRP A 276 
 HIS   0.005   0.002   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3247)
  covalent geometry    : angle       0.52892 ( 4403)
  hydrogen bonds       : bond        0.03506 (  192)
  hydrogen bonds       : angle       4.29347 (  567)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  205 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8278 (pmm)
REVERT: A  248 MET cc_start: 0.9188 (tpp) cc_final: 0.8957 (mmm)
REVERT: A  255 MET cc_start: 0.8999 (tpp) cc_final: 0.8486 (mmp)
REVERT: A  284 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8058 (tt)
REVERT: A  328 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7832 (tt)
REVERT: A  455 ASP cc_start: 0.8220 (m-30) cc_final: 0.7971 (m-30)
  outliers start: 12
  outliers final: 7
  residues processed: 65
  average time/residue: 0.0320
  time to fit residues: 3.0240
Evaluate side-chains
  66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  426 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0030
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 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 = 0.3790 r_free = 0.3790 target = 0.142890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.107033 restraints weight = 4627.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.19
r_work: 0.3117 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3247  Z= 0.106
  Angle     :  0.512   7.536   4403  Z= 0.263
  Chirality :  0.040   0.169    558
  Planarity :  0.003   0.027    537
  Dihedral  :  4.567  27.160    440
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 24.93 %
    Favored  : 72.52 %
  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: -0.37 (0.43), residues: 413
  helix:  0.24 (0.31), residues: 309
  sheet: -0.16 (1.45), residues: 18
  loop : -1.70 (0.62), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 447 
 TYR   0.005   0.001   TYR A  97 
 PHE   0.011   0.001   PHE A 218 
 TRP   0.005   0.001   TRP A 276 
 HIS   0.004   0.002   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 3247)
  covalent geometry    : angle       0.51242 ( 4403)
  hydrogen bonds       : bond        0.03186 (  192)
  hydrogen bonds       : angle       4.07332 (  567)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A  248 MET cc_start: 0.9105 (tpp) cc_final: 0.8891 (mmm)
REVERT: A  255 MET cc_start: 0.9001 (tpp) cc_final: 0.8549 (mmp)
REVERT: A  284 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8029 (tt)
REVERT: A  455 ASP cc_start: 0.8241 (m-30) cc_final: 0.8025 (m-30)
  outliers start: 9
  outliers final: 6
  residues processed: 65
  average time/residue: 0.0317
  time to fit residues: 2.9978
Evaluate side-chains
  61 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  426 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 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 = 0.3760 r_free = 0.3760 target = 0.140803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.104293 restraints weight = 4660.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.22
r_work: 0.3113 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3247  Z= 0.125
  Angle     :  0.542  10.474   4403  Z= 0.272
  Chirality :  0.040   0.134    558
  Planarity :  0.003   0.027    537
  Dihedral  :  4.526  24.924    440
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 24.36 %
    Favored  : 71.95 %
  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: -0.18 (0.43), residues: 413
  helix:  0.35 (0.31), residues: 315
  sheet: -0.08 (1.44), residues: 18
  loop : -1.61 (0.66), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  93 
 TYR   0.006   0.001   TYR A  97 
 PHE   0.011   0.001   PHE A 218 
 TRP   0.004   0.001   TRP A 276 
 HIS   0.004   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3247)
  covalent geometry    : angle       0.54213 ( 4403)
  hydrogen bonds       : bond        0.03236 (  192)
  hydrogen bonds       : angle       4.03346 (  567)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  248 MET cc_start: 0.9112 (tpp) cc_final: 0.8900 (mmm)
REVERT: A  284 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8005 (tt)
REVERT: A  419 MET cc_start: 0.9154 (tpt) cc_final: 0.8308 (tpt)
  outliers start: 13
  outliers final: 7
  residues processed: 65
  average time/residue: 0.0329
  time to fit residues: 3.1048
Evaluate side-chains
  62 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  475 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 18 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 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 = 0.3823 r_free = 0.3823 target = 0.145310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.110009 restraints weight = 4717.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.19
r_work: 0.3125 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3247  Z= 0.105
  Angle     :  0.537   9.837   4403  Z= 0.269
  Chirality :  0.040   0.133    558
  Planarity :  0.003   0.027    537
  Dihedral  :  4.412  23.842    440
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 25.21 %
    Favored  : 72.24 %
  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:  0.14 (0.43), residues: 413
  helix:  0.67 (0.32), residues: 307
  sheet: -0.18 (1.43), residues: 18
  loop : -1.70 (0.60), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  93 
 TYR   0.006   0.001   TYR A  97 
 PHE   0.010   0.001   PHE A 218 
 TRP   0.005   0.001   TRP A 276 
 HIS   0.004   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 3247)
  covalent geometry    : angle       0.53693 ( 4403)
  hydrogen bonds       : bond        0.03079 (  192)
  hydrogen bonds       : angle       3.93969 (  567)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  248 MET cc_start: 0.9030 (tpp) cc_final: 0.8791 (mmm)
REVERT: A  284 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7928 (tt)
REVERT: A  384 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7570 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 65
  average time/residue: 0.0322
  time to fit residues: 3.0541
Evaluate side-chains
  65 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  426 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 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 = 0.3834 r_free = 0.3834 target = 0.145784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.110573 restraints weight = 4755.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.20
r_work: 0.3148 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3247  Z= 0.116
  Angle     :  0.549   9.275   4403  Z= 0.277
  Chirality :  0.040   0.131    558
  Planarity :  0.003   0.027    537
  Dihedral  :  4.492  29.874    440
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 24.36 %
    Favored  : 72.52 %
  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:  0.22 (0.43), residues: 413
  helix:  0.74 (0.31), residues: 307
  sheet: -0.18 (1.40), residues: 18
  loop : -1.67 (0.60), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  93 
 TYR   0.012   0.001   TYR A  97 
 PHE   0.013   0.001   PHE A 316 
 TRP   0.004   0.000   TRP A 276 
 HIS   0.003   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3247)
  covalent geometry    : angle       0.54938 ( 4403)
  hydrogen bonds       : bond        0.03237 (  192)
  hydrogen bonds       : angle       3.96022 (  567)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  248 MET cc_start: 0.9051 (tpp) cc_final: 0.8834 (mmm)
REVERT: A  277 GLU cc_start: 0.8588 (tp30) cc_final: 0.8210 (tp30)
REVERT: A  284 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7989 (tt)
REVERT: A  384 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7687 (mp)
REVERT: A  419 MET cc_start: 0.9134 (tpt) cc_final: 0.8815 (tpt)
  outliers start: 11
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0330
  time to fit residues: 2.9889
Evaluate side-chains
  66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  475 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0870
   chunk 18 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 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 = 0.3845 r_free = 0.3845 target = 0.146992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.111481 restraints weight = 4659.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.20
r_work: 0.3153 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3247  Z= 0.100
  Angle     :  0.532   8.966   4403  Z= 0.268
  Chirality :  0.039   0.136    558
  Planarity :  0.003   0.026    537
  Dihedral  :  4.415  31.952    440
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 25.21 %
    Favored  : 72.52 %
  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:  0.48 (0.43), residues: 413
  helix:  0.91 (0.31), residues: 309
  sheet: -0.06 (1.39), residues: 18
  loop : -1.59 (0.60), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 342 
 TYR   0.011   0.001   TYR A  97 
 PHE   0.014   0.001   PHE A 316 
 TRP   0.004   0.000   TRP A 276 
 HIS   0.004   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 3247)
  covalent geometry    : angle       0.53173 ( 4403)
  hydrogen bonds       : bond        0.03058 (  192)
  hydrogen bonds       : angle       3.87419 (  567)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A  277 GLU cc_start: 0.8564 (tp30) cc_final: 0.8188 (tp30)
REVERT: A  284 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7882 (tt)
REVERT: A  384 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7613 (mp)
REVERT: A  419 MET cc_start: 0.9074 (tpt) cc_final: 0.8351 (tpt)
  outliers start: 8
  outliers final: 4
  residues processed: 61
  average time/residue: 0.0315
  time to fit residues: 2.7991
Evaluate side-chains
  61 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  426 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 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 = 0.3844 r_free = 0.3844 target = 0.146803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.111532 restraints weight = 4541.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.13
r_work: 0.3143 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3247  Z= 0.110
  Angle     :  0.545   9.140   4403  Z= 0.274
  Chirality :  0.040   0.134    558
  Planarity :  0.003   0.026    537
  Dihedral  :  4.410  32.007    440
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 26.06 %
    Favored  : 71.67 %
  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:  0.57 (0.43), residues: 413
  helix:  1.00 (0.31), residues: 309
  sheet: -0.29 (1.31), residues: 18
  loop : -1.55 (0.60), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  93 
 TYR   0.004   0.001   TYR A 257 
 PHE   0.014   0.001   PHE A 316 
 TRP   0.004   0.000   TRP A 276 
 HIS   0.003   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3247)
  covalent geometry    : angle       0.54545 ( 4403)
  hydrogen bonds       : bond        0.03174 (  192)
  hydrogen bonds       : angle       3.85229 (  567)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  277 GLU cc_start: 0.8554 (tp30) cc_final: 0.8152 (tp30)
REVERT: A  284 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7915 (tt)
REVERT: A  384 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7706 (mp)
REVERT: A  419 MET cc_start: 0.9084 (tpt) cc_final: 0.8813 (tpt)
  outliers start: 8
  outliers final: 5
  residues processed: 62
  average time/residue: 0.0347
  time to fit residues: 3.0489
Evaluate side-chains
  62 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  426 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0060
   chunk 40 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   chunk 33 optimal weight:    0.0020
   chunk 38 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0040
   overall best weight:    0.2216

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

Flipped N/Q/H residues before XYZ refinement:
A 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.150753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.115353 restraints weight = 4653.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.17
r_work: 0.3252 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3247  Z= 0.094
  Angle     :  0.541   8.884   4403  Z= 0.267
  Chirality :  0.039   0.141    558
  Planarity :  0.003   0.026    537
  Dihedral  :  4.296  33.632    440
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 25.78 %
    Favored  : 72.52 %
  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:  0.76 (0.43), residues: 413
  helix:  1.13 (0.31), residues: 310
  sheet: -0.27 (1.24), residues: 18
  loop : -1.50 (0.60), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 342 
 TYR   0.008   0.001   TYR A  97 
 PHE   0.018   0.001   PHE A 316 
 TRP   0.004   0.000   TRP A 276 
 HIS   0.004   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 ( 3247)
  covalent geometry    : angle       0.54053 ( 4403)
  hydrogen bonds       : bond        0.02874 (  192)
  hydrogen bonds       : angle       3.72893 (  567)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1108.54 seconds
wall clock time: 19 minutes 30.40 seconds (1170.40 seconds total)