Starting phenix.real_space_refine
on Wed Jul  1 23:22:46 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7xkw_33209/07_2026/7xkw_33209.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xkw_33209/07_2026/7xkw_33209.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7xkw_33209/07_2026/7xkw_33209.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7xkw_33209/07_2026/7xkw_33209.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xkw_33209/07_2026/7xkw_33209.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xkw_33209/07_2026/7xkw_33209.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xkw_33209/07_2026/7xkw_33209.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xkw_33209/07_2026/7xkw_33209.cif"
  }
  resolution = 3.1
  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=   0.104
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      3      5.21       5
     S      21      5.16       5
     C    2632      2.51       5
     N     706      2.21       5
     O     768      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4132
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4105
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 499, 4097
          Classifications: {'peptide': 499}
          Link IDs: {'PTRANS': 14, 'TRANS': 484}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 499, 4097
          Classifications: {'peptide': 499}
          Link IDs: {'PTRANS': 14, 'TRANS': 484}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4168
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 27
          Unusual residues: {' MG': 3, 'FPS': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.88, per 1000 atoms: 0.45
  Number of scatterers: 4132
  At special positions: 0
  Unit cell: (63.18, 78.57, 87.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      21     16.00
     P       2     15.00
     Mg      3     11.99
     O     768      8.00
     N     706      7.00
     C    2632      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: 0.39
  Conformation dependent library (CDL) restraints added in 287.2 milliseconds
  

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  972

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      79.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 74
    Processing helix  chain 'A' and resid 77 through 90
      removed outlier: 3.986A  pdb=" N   LEU A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 95
    Processing helix  chain 'A' and resid 96 through 110
    Processing helix  chain 'A' and resid 121 through 136
      removed outlier: 3.603A  pdb=" N   HIS A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 146
      removed outlier: 3.927A  pdb=" N   LYS A 146 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 159
    Processing helix  chain 'A' and resid 161 through 173
      removed outlier: 3.786A  pdb=" N   TYR A 173 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 197
      removed outlier: 4.114A  pdb=" N   ALA A 187 " --> pdb=" O   ASP A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 214
      removed outlier: 4.334A  pdb=" N   LEU A 207 " --> pdb=" O   PRO A 203 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ASP A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   LEU A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 233
      removed outlier: 3.947A  pdb=" N   GLN A 233 " --> pdb=" O   ILE A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 271
      removed outlier: 3.638A  pdb=" N   ASN A 262 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU A 263 " --> pdb=" O   LYS A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 289
    Processing helix  chain 'A' and resid 297 through 299
      No H-bonds generated for 'chain 'A' and resid 297 through 299'
    Processing helix  chain 'A' and resid 300 through 323
      removed outlier: 3.708A  pdb=" N   MET A 306 " --> pdb=" O   GLN A 302 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   THR A 307 " --> pdb=" O   SER A 303 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU A 310 " --> pdb=" O   MET A 306 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE A 312 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LEU A 313 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   THR A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASP A 318 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 340
      removed outlier: 3.982A  pdb=" N   ARG A 332 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   TYR A 333 " --> pdb=" O   GLU A 329 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   VAL A 335 " --> pdb=" O   GLU A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 346
    Processing helix  chain 'A' and resid 349 through 371
    Processing helix  chain 'A' and resid 375 through 377
      No H-bonds generated for 'chain 'A' and resid 375 through 377'
    Processing helix  chain 'A' and resid 378 through 403
      removed outlier: 3.617A  pdb=" N   VAL A 382 " --> pdb=" O   HIS A 378 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   LYS A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LYS A 395 " --> pdb=" O   LYS A 391 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ARG A 398 " --> pdb=" O   ILE A 394 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU A 403 " --> pdb=" O   TRP A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 418
      removed outlier: 4.178A  pdb=" N   VAL A 417 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 428
    Processing helix  chain 'A' and resid 429 through 432
    Processing helix  chain 'A' and resid 437 through 446
    Processing helix  chain 'A' and resid 448 through 467
      removed outlier: 4.123A  pdb=" N   ILE A 457 " --> pdb=" O   GLN A 453 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   CYS A 458 " --> pdb=" O   CYS A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 473
      removed outlier: 3.743A  pdb=" N   GLU A 472 " --> pdb=" O   SER A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 486
      removed outlier: 3.843A  pdb=" N   GLU A 486 " --> pdb=" O   CYS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 513
      removed outlier: 3.552A  pdb=" N   LYS A 501 " --> pdb=" O   ILE A 497 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ILE A 502 " --> pdb=" O   LEU A 498 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ALA A 503 " --> pdb=" O   GLN A 499 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ARG A 504 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LYS A 511 " --> pdb=" O   LYS A 507 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU A 512 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   CYS A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 538
      removed outlier: 4.288A  pdb=" N   ARG A 526 " --> pdb=" O   GLU A 522 " (cutoff:3.500A)
      Proline residue:  A 527  - end of helix
      removed outlier: 3.789A  pdb=" N   ILE A 534 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLU A 535 " --> pdb=" O   ALA A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 559

    237 hydrogen bonds defined for protein.
    683 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: 0.63

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.18 -     1.36: 1379
        1.36 -     1.54: 2731
        1.54 -     1.71: 65
        1.71 -     1.89: 33
        1.89 -     2.07: 1
  Bond restraints: 4209
  Sorted by residual:
  bond pdb=" O3A FPS A 601 "
       pdb=" PB  FPS A 601 "
    ideal  model  delta    sigma   weight residual
    1.760  1.598  0.162 2.00e-02 2.50e+03 6.56e+01
  bond pdb=" PA  FPS A 601 "
       pdb=" S1  FPS A 601 "
    ideal  model  delta    sigma   weight residual
    2.179  2.069  0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" CA  SER A 419 "
       pdb=" CB  SER A 419 "
    ideal  model  delta    sigma   weight residual
    1.534  1.455  0.079 1.58e-02 4.01e+03 2.49e+01
  bond pdb=" CA  ALA A 420 "
       pdb=" CB  ALA A 420 "
    ideal  model  delta    sigma   weight residual
    1.531  1.458  0.074 1.53e-02 4.27e+03 2.33e+01
  bond pdb=" CA  SER A 418 "
       pdb=" CB  SER A 418 "
    ideal  model  delta    sigma   weight residual
    1.531  1.453  0.078 1.69e-02 3.50e+03 2.12e+01
  ... (remaining 4204 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 5413
        2.11 -     4.22: 220
        4.22 -     6.33: 46
        6.33 -     8.45: 6
        8.45 -    10.56: 2
  Bond angle restraints: 5687
  Sorted by residual:
  angle pdb=" N   TRP A 290 "
        pdb=" CA  TRP A 290 "
        pdb=" C   TRP A 290 "
      ideal   model   delta    sigma   weight residual
     113.23  105.18    8.05 1.24e+00 6.50e-01 4.21e+01
  angle pdb=" N   SER A 419 "
        pdb=" CA  SER A 419 "
        pdb=" C   SER A 419 "
      ideal   model   delta    sigma   weight residual
     113.50  105.84    7.66 1.23e+00 6.61e-01 3.88e+01
  angle pdb=" CA  ILE A 457 "
        pdb=" C   ILE A 457 "
        pdb=" N   CYS A 458 "
      ideal   model   delta    sigma   weight residual
     116.72  122.43   -5.71 1.10e+00 8.26e-01 2.69e+01
  angle pdb=" CA  TYR A 393 "
        pdb=" C   TYR A 393 "
        pdb=" O   TYR A 393 "
      ideal   model   delta    sigma   weight residual
     120.55  115.21    5.34 1.06e+00 8.90e-01 2.54e+01
  angle pdb=" CA  TYR A 538 "
        pdb=" C   TYR A 538 "
        pdb=" O   TYR A 538 "
      ideal   model   delta    sigma   weight residual
     122.64  116.38    6.26 1.25e+00 6.40e-01 2.51e+01
  ... (remaining 5682 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 2324
       17.28 -    34.56: 195
       34.56 -    51.84: 49
       51.84 -    69.12: 10
       69.12 -    86.39: 3
  Dihedral angle restraints: 2581
    sinusoidal: 1088
      harmonic: 1493
  Sorted by residual:
  dihedral pdb=" C   GLU A 328 "
           pdb=" N   GLU A 328 "
           pdb=" CA  GLU A 328 "
           pdb=" CB  GLU A 328 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.51   -9.09     0      2.50e+00 1.60e-01 1.32e+01
  dihedral pdb=" C   TYR A 537 "
           pdb=" N   TYR A 537 "
           pdb=" CA  TYR A 537 "
           pdb=" CB  TYR A 537 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.65   -8.95     0      2.50e+00 1.60e-01 1.28e+01
  dihedral pdb=" N   GLU A 328 "
           pdb=" C   GLU A 328 "
           pdb=" CA  GLU A 328 "
           pdb=" CB  GLU A 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.78    8.02     0      2.50e+00 1.60e-01 1.03e+01
  ... (remaining 2578 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 550
       0.072 -    0.144: 60
       0.144 -    0.216: 16
       0.216 -    0.288: 2
       0.288 -    0.360: 1
  Chirality restraints: 629
  Sorted by residual:
  chirality pdb=" CA  GLU A 328 "
            pdb=" N   GLU A 328 "
            pdb=" C   GLU A 328 "
            pdb=" CB  GLU A 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" CA  ARG A 281 "
            pdb=" N   ARG A 281 "
            pdb=" C   ARG A 281 "
            pdb=" CB  ARG A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CA  TYR A 538 "
            pdb=" N   TYR A 538 "
            pdb=" C   TYR A 538 "
            pdb=" CB  TYR A 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 626 not shown)

  Planarity restraints: 727
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 515 "   -0.051 5.00e-02 4.00e+02   7.84e-02 9.83e+00
        pdb=" N   PRO A 516 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 516 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 516 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 326 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.70e+00
        pdb=" C   LYS A 326 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LYS A 326 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU A 327 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 309 "    0.013 2.00e-02 2.50e+03   2.57e-02 6.59e+00
        pdb=" C   ILE A 309 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ILE A 309 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LEU A 310 "    0.015 2.00e-02 2.50e+03
  ... (remaining 724 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 1
        2.22 -     2.89: 1523
        2.89 -     3.56: 5999
        3.56 -     4.23: 9238
        4.23 -     4.90: 16532
  Nonbonded interactions: 33293
  Sorted by model distance:
  nonbonded pdb=" O2B FPS A 601 "
            pdb="MG    MG A 603 "
     model   vdw
     1.547 2.170
  nonbonded pdb=" OD1 ASP A 318 "
            pdb="MG    MG A 603 "
     model   vdw
     2.233 2.170
  nonbonded pdb=" O   GLU A  61 "
            pdb=" NE2 GLN A  65 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" NH2 ARG A 332 "
            pdb=" O   GLN A 347 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" OD1 ASP A 272 "
            pdb=" NH1 ARG A 275 "
     model   vdw
     2.307 3.120
  ... (remaining 33288 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=0.50 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:             1.350
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.040
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
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      :  0.007   0.162   4209  Z= 0.473
  Angle     :  0.961  10.558   5687  Z= 0.640
  Chirality :  0.055   0.360    629
  Planarity :  0.006   0.078    727
  Dihedral  : 14.154  86.394   1609
  Min Nonbonded Distance : 1.547

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  3.03 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  2.23 %
    Favored  : 96.66 %
  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: -1.01 (0.38), residues: 496
  helix: -0.13 (0.28), residues: 362
  sheet:  None (None), residues: 0
  loop : -1.93 (0.51), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 133 
 TYR   0.024   0.002   TYR A 538 
 PHE   0.007   0.001   PHE A 147 
 TRP   0.023   0.002   TRP A 290 
 HIS   0.009   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00698 /  0.47 ( 4209)
  covalent geometry    : angle       0.96127 /  0.64 ( 5687)
  hydrogen bonds       : bond        0.21663 / 15.25 (  237)
  hydrogen bonds       : angle       6.68227 /  5.03 (  683)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.8532 (mmm) cc_final: 0.7978 (mmp)
  outliers start: 5
  outliers final: 2
  residues processed: 66
  average time/residue: 0.0874
  time to fit residues: 7.1004
Evaluate side-chains
  44 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  470 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  72 HIS
A 401 ASN
A 481 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.172385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.136404 restraints weight = 13903.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 4.02
r_work: 0.3257 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4209  Z= 0.134
  Angle     :  0.567   5.701   5687  Z= 0.297
  Chirality :  0.039   0.118    629
  Planarity :  0.005   0.074    727
  Dihedral  :  6.996  59.019    577
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  7.13 %
    Favored  : 92.65 %
  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: -0.24 (0.38), residues: 496
  helix:  0.43 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -1.61 (0.52), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 304 
 TYR   0.021   0.002   TYR A 232 
 PHE   0.009   0.001   PHE A 377 
 TRP   0.018   0.002   TRP A 399 
 HIS   0.007   0.002   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 4209)
  covalent geometry    : angle       0.56658 /  0.30 ( 5687)
  hydrogen bonds       : bond        0.04809 /  3.24 (  237)
  hydrogen bonds       : angle       4.12703 /  3.12 (  683)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  291 MET cc_start: 0.8625 (mmm) cc_final: 0.8109 (mmp)
REVERT: A  442 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7591 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0891
  time to fit residues: 5.8908
Evaluate side-chains
  48 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.165899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.128468 restraints weight = 7721.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.90
r_work: 0.3270 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4209  Z= 0.133
  Angle     :  0.539   5.587   5687  Z= 0.282
  Chirality :  0.039   0.145    629
  Planarity :  0.005   0.064    727
  Dihedral  :  6.598  59.408    573
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  6.90 %
    Favored  : 91.76 %
  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:  0.10 (0.38), residues: 496
  helix:  0.71 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -1.56 (0.52), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 130 
 TYR   0.021   0.002   TYR A 232 
 PHE   0.011   0.001   PHE A 377 
 TRP   0.014   0.001   TRP A 399 
 HIS   0.006   0.002   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 ( 4209)
  covalent geometry    : angle       0.53936 /  0.28 ( 5687)
  hydrogen bonds       : bond        0.04798 /  3.22 (  237)
  hydrogen bonds       : angle       3.89002 /  2.95 (  683)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  236 GLU cc_start: 0.7545 (mp0) cc_final: 0.7212 (mp0)
REVERT: A  442 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7582 (mt-10)
REVERT: A  539 GLN cc_start: 0.5655 (mm-40) cc_final: 0.5384 (mm-40)
REVERT: A  553 ASP cc_start: 0.4051 (p0) cc_final: 0.3732 (p0)
  outliers start: 6
  outliers final: 5
  residues processed: 55
  average time/residue: 0.0773
  time to fit residues: 5.4330
Evaluate side-chains
  51 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  515 HIS
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  65 GLN
A  72 HIS
A 262 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.165040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.127388 restraints weight = 7710.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.89
r_work: 0.3231 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4209  Z= 0.130
  Angle     :  0.521   5.631   5687  Z= 0.272
  Chirality :  0.039   0.141    629
  Planarity :  0.004   0.062    727
  Dihedral  :  6.457  59.815    573
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  7.13 %
    Favored  : 91.31 %
  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:  0.38 (0.38), residues: 496
  helix:  0.94 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -1.53 (0.52), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 304 
 TYR   0.019   0.002   TYR A 232 
 PHE   0.010   0.001   PHE A 377 
 TRP   0.013   0.001   TRP A 399 
 HIS   0.006   0.002   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 4209)
  covalent geometry    : angle       0.52142 /  0.27 ( 5687)
  hydrogen bonds       : bond        0.04590 /  3.06 (  237)
  hydrogen bonds       : angle       3.77277 /  2.86 (  683)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  236 GLU cc_start: 0.7568 (mp0) cc_final: 0.7226 (mp0)
REVERT: A  331 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7315 (mt-10)
REVERT: A  372 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7393 (mmmt)
REVERT: A  553 ASP cc_start: 0.4039 (p0) cc_final: 0.3749 (p0)
  outliers start: 7
  outliers final: 5
  residues processed: 52
  average time/residue: 0.0795
  time to fit residues: 5.1980
Evaluate side-chains
  49 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 27 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  72 HIS
A 262 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.165692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.127956 restraints weight = 10722.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 3.16
r_work: 0.3215 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4209  Z= 0.121
  Angle     :  0.507   5.400   5687  Z= 0.265
  Chirality :  0.038   0.138    629
  Planarity :  0.004   0.058    727
  Dihedral  :  6.303  59.656    573
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  8.24 %
    Favored  : 90.20 %
  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:  0.60 (0.38), residues: 496
  helix:  1.12 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -1.52 (0.52), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 304 
 TYR   0.017   0.002   TYR A 232 
 PHE   0.009   0.001   PHE A 377 
 TRP   0.011   0.001   TRP A 399 
 HIS   0.007   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 4209)
  covalent geometry    : angle       0.50742 /  0.26 ( 5687)
  hydrogen bonds       : bond        0.04312 /  2.87 (  237)
  hydrogen bonds       : angle       3.67884 /  2.81 (  683)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  159 ARG cc_start: 0.7482 (mtp-110) cc_final: 0.7269 (mtp-110)
REVERT: A  236 GLU cc_start: 0.7673 (mp0) cc_final: 0.7367 (mp0)
REVERT: A  291 MET cc_start: 0.8624 (mmp) cc_final: 0.8142 (mmt)
REVERT: A  331 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7334 (mt-10)
REVERT: A  372 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7352 (mmmt)
REVERT: A  553 ASP cc_start: 0.4069 (p0) cc_final: 0.3754 (p0)
  outliers start: 7
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0721
  time to fit residues: 4.9841
Evaluate side-chains
  53 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  515 HIS
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 6 optimal weight:    0.0070
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0060
   chunk 20 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.4814

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  65 GLN
A  72 HIS
A 262 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.168534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.130767 restraints weight = 9886.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 3.06
r_work: 0.3249 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3243
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3243
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4209  Z= 0.104
  Angle     :  0.478   5.236   5687  Z= 0.250
  Chirality :  0.037   0.115    629
  Planarity :  0.004   0.059    727
  Dihedral  :  6.099  59.421    573
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  8.02 %
    Favored  : 90.20 %
  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:  0.84 (0.39), residues: 496
  helix:  1.33 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -1.52 (0.52), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 304 
 TYR   0.014   0.001   TYR A 232 
 PHE   0.009   0.001   PHE A 377 
 TRP   0.009   0.001   TRP A 399 
 HIS   0.007   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00224 /  0.10 ( 4209)
  covalent geometry    : angle       0.47815 /  0.25 ( 5687)
  hydrogen bonds       : bond        0.03814 /  2.54 (  237)
  hydrogen bonds       : angle       3.54464 /  2.72 (  683)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A  236 GLU cc_start: 0.7660 (mp0) cc_final: 0.7362 (mp0)
REVERT: A  331 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7320 (mm-30)
REVERT: A  553 ASP cc_start: 0.4307 (p0) cc_final: 0.3951 (p0)
  outliers start: 8
  outliers final: 5
  residues processed: 55
  average time/residue: 0.0835
  time to fit residues: 5.7569
Evaluate side-chains
  51 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  515 HIS
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  65 GLN
A  72 HIS
A 262 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.165435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.126645 restraints weight = 11581.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 3.35
r_work: 0.3203 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4209  Z= 0.125
  Angle     :  0.512   5.463   5687  Z= 0.267
  Chirality :  0.038   0.138    629
  Planarity :  0.004   0.057    727
  Dihedral  :  5.987  58.151    573
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  8.69 %
    Favored  : 89.53 %
  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:  0.77 (0.38), residues: 496
  helix:  1.26 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -1.50 (0.52), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 304 
 TYR   0.017   0.002   TYR A 232 
 PHE   0.009   0.001   PHE A 377 
 TRP   0.009   0.001   TRP A 399 
 HIS   0.007   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 4209)
  covalent geometry    : angle       0.51187 /  0.27 ( 5687)
  hydrogen bonds       : bond        0.04289 /  2.85 (  237)
  hydrogen bonds       : angle       3.62443 /  2.77 (  683)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7329 (mt-10)
REVERT: A  553 ASP cc_start: 0.4519 (p0) cc_final: 0.4158 (p0)
  outliers start: 8
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0803
  time to fit residues: 5.2373
Evaluate side-chains
  51 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  65 GLN
A  72 HIS
A 262 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.175837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.140376 restraints weight = 13173.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 3.25
r_work: 0.3210 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3210
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4209  Z= 0.130
  Angle     :  0.521   5.690   5687  Z= 0.272
  Chirality :  0.038   0.146    629
  Planarity :  0.004   0.056    727
  Dihedral  :  5.940  57.211    573
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  8.46 %
    Favored  : 89.31 %
  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:  0.76 (0.38), residues: 496
  helix:  1.26 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -1.53 (0.52), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 281 
 TYR   0.018   0.002   TYR A 232 
 PHE   0.010   0.001   PHE A 377 
 TRP   0.009   0.001   TRP A 399 
 HIS   0.007   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 ( 4209)
  covalent geometry    : angle       0.52105 /  0.27 ( 5687)
  hydrogen bonds       : bond        0.04436 /  2.95 (  237)
  hydrogen bonds       : angle       3.65270 /  2.79 (  683)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 GLU cc_start: 0.7551 (pm20) cc_final: 0.7324 (pm20)
REVERT: A  331 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7255 (mt-10)
REVERT: A  486 GLU cc_start: 0.5062 (pm20) cc_final: 0.4835 (pm20)
REVERT: A  553 ASP cc_start: 0.4388 (p0) cc_final: 0.4039 (p0)
  outliers start: 10
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0795
  time to fit residues: 5.1510
Evaluate side-chains
  52 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  65 GLN
A  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.163916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.126400 restraints weight = 7774.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.89
r_work: 0.3223 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4209  Z= 0.133
  Angle     :  0.527   5.780   5687  Z= 0.275
  Chirality :  0.038   0.150    629
  Planarity :  0.004   0.056    727
  Dihedral  :  5.942  57.022    573
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  9.35 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.73 (0.38), residues: 496
  helix:  1.23 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -1.55 (0.52), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 304 
 TYR   0.017   0.002   TYR A 232 
 PHE   0.010   0.001   PHE A 377 
 TRP   0.009   0.001   TRP A 399 
 HIS   0.007   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 4209)
  covalent geometry    : angle       0.52696 /  0.28 ( 5687)
  hydrogen bonds       : bond        0.04486 /  2.98 (  237)
  hydrogen bonds       : angle       3.64932 /  2.78 (  683)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 GLU cc_start: 0.7573 (pm20) cc_final: 0.7340 (pm20)
REVERT: A  331 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7286 (mt-10)
REVERT: A  486 GLU cc_start: 0.5043 (pm20) cc_final: 0.4810 (pm20)
REVERT: A  553 ASP cc_start: 0.4471 (p0) cc_final: 0.4085 (p0)
  outliers start: 8
  outliers final: 7
  residues processed: 50
  average time/residue: 0.0765
  time to fit residues: 4.8312
Evaluate side-chains
  50 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.2980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  65 GLN
A  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.168217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.131793 restraints weight = 10901.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.93
r_work: 0.3225 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4209  Z= 0.119
  Angle     :  0.511   5.429   5687  Z= 0.267
  Chirality :  0.038   0.138    629
  Planarity :  0.004   0.056    727
  Dihedral  :  5.892  57.098    573
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  9.35 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.83 (0.39), residues: 496
  helix:  1.32 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -1.54 (0.52), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 304 
 TYR   0.015   0.002   TYR A 232 
 PHE   0.010   0.001   PHE A 377 
 TRP   0.009   0.001   TRP A 399 
 HIS   0.007   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 4209)
  covalent geometry    : angle       0.51139 /  0.27 ( 5687)
  hydrogen bonds       : bond        0.04172 /  2.78 (  237)
  hydrogen bonds       : angle       3.58419 /  2.74 (  683)

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

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

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  992 Ramachandran restraints generated.
    496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 GLU cc_start: 0.7546 (pm20) cc_final: 0.7318 (pm20)
REVERT: A  331 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7216 (mt-10)
REVERT: A  486 GLU cc_start: 0.4982 (pm20) cc_final: 0.4754 (pm20)
REVERT: A  553 ASP cc_start: 0.4443 (p0) cc_final: 0.4060 (p0)
  outliers start: 8
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0664
  time to fit residues: 4.3090
Evaluate side-chains
  52 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0040
   overall best weight:    0.6592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  65 GLN
A  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.168439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.131204 restraints weight = 13995.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 3.74
r_work: 0.3199 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4209  Z= 0.118
  Angle     :  0.509   5.350   5687  Z= 0.266
  Chirality :  0.037   0.135    629
  Planarity :  0.004   0.056    727
  Dihedral  :  5.861  57.162    573
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  9.35 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.83 (0.39), residues: 496
  helix:  1.33 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -1.58 (0.52), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 304 
 TYR   0.016   0.002   TYR A 232 
 PHE   0.010   0.001   PHE A 377 
 TRP   0.009   0.001   TRP A 399 
 HIS   0.007   0.001   HIS A  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 4209)
  covalent geometry    : angle       0.50922 /  0.27 ( 5687)
  hydrogen bonds       : bond        0.04126 /  2.75 (  237)
  hydrogen bonds       : angle       3.57064 /  2.73 (  683)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1206.69 seconds
wall clock time: 21 minutes 24.51 seconds (1284.51 seconds total)