Starting phenix.real_space_refine
on Sat May  2 14:08:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v65_64797/05_2026/9v65_64797.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v65_64797/05_2026/9v65_64797.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v65_64797/05_2026/9v65_64797.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v65_64797/05_2026/9v65_64797.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v65_64797/05_2026/9v65_64797.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v65_64797/05_2026/9v65_64797.cif"
  }
  resolution = 3.2
  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=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    3910      2.51       5
     N    1132      2.21       5
     O    1152      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6210
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 779, 6209
          Classifications: {'peptide': 779}
          Link IDs: {'PTRANS': 44, 'TRANS': 734}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.62, per 1000 atoms: 0.26
  Number of scatterers: 6210
  At special positions: 0
  Unit cell: (81.696, 85.1, 92.759, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O    1152      8.00
     N    1132      7.00
     C    3910      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: 0.38
  Conformation dependent library (CDL) restraints added in 339.3 milliseconds
  

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1450

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 7 sheets defined
      28.4% alpha, 25.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 54
      removed outlier: 3.593A  pdb=" N   ARG A  41 " --> pdb=" O   GLN A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
      removed outlier: 3.528A  pdb=" N   ARG A 130 " --> pdb=" O   ASP A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 202
    Processing helix  chain 'A' and resid 203 through 208
    Processing helix  chain 'A' and resid 254 through 263
    Processing helix  chain 'A' and resid 299 through 304
    Processing helix  chain 'A' and resid 312 through 324
      removed outlier: 3.625A  pdb=" N   VAL A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ARG A 321 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ALA A 322 " --> pdb=" O   GLU A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 328
      removed outlier: 3.775A  pdb=" N   ARG A 328 " --> pdb=" O   ASN A 325 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 325 through 328'
    Processing helix  chain 'A' and resid 372 through 391
      removed outlier: 3.813A  pdb=" N   MET A 385 " --> pdb=" O   ARG A 381 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LEU A 388 " --> pdb=" O   LYS A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 430
      removed outlier: 3.510A  pdb=" N   GLU A 424 " --> pdb=" O   GLN A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 464
    Processing helix  chain 'A' and resid 482 through 491
      removed outlier: 3.912A  pdb=" N   LEU A 486 " --> pdb=" O   HIS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 510
    Processing helix  chain 'A' and resid 519 through 531
      removed outlier: 3.650A  pdb=" N   GLY A 531 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 605
      removed outlier: 3.696A  pdb=" N   ALA A 592 " --> pdb=" O   ARG A 588 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   GLN A 594 " --> pdb=" O   GLN A 590 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU A 605 " --> pdb=" O   GLU A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 639
    Processing helix  chain 'A' and resid 723 through 736
      removed outlier: 3.576A  pdb=" N   GLU A 729 " --> pdb=" O   ARG A 725 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   HIS A 736 " --> pdb=" O   TYR A 732 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346
      removed outlier: 3.517A  pdb=" N   SER A 663 " --> pdb=" O   GLU A 673 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139
      removed outlier: 6.746A  pdb=" N   LEU A 142 " --> pdb=" O   LYS A 138 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ARG A 162 " --> pdb=" O   ARG A 145 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU A 171 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LYS A 174 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   TYR A 185 " --> pdb=" O   PHE A 295 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   PHE A 274 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   SER A 235 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   ALA A 272 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A 275 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 139
      removed outlier: 6.746A  pdb=" N   LEU A 142 " --> pdb=" O   LYS A 138 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ARG A 162 " --> pdb=" O   ARG A 145 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU A 171 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LYS A 174 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   VAL A 330 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 60
      removed outlier: 3.711A  pdb=" N   VAL A  58 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   VAL A  25 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   GLU A  99 " --> pdb=" O   VAL A  25 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ARG A  27 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ILE A  97 " --> pdb=" O   ARG A  27 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   TYR A  92 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL A  84 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 247
      removed outlier: 3.605A  pdb=" N   LYS A 252 " --> pdb=" O   PHE A 245 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 438 through 442
      removed outlier: 7.426A  pdb=" N   LEU A 402 " --> pdb=" O   ARG A 438 " (cutoff:3.500A)
      removed outlier: 8.322A  pdb=" N   ILE A 440 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   LEU A 404 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   TYR A 442 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   TYR A 406 " --> pdb=" O   TYR A 442 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ASP A 401 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   VAL A 472 " --> pdb=" O   ASP A 401 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   VAL A 403 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   VAL A 474 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   LEU A 405 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   VAL A 499 " --> pdb=" O   PRO A 471 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ILE A 473 " --> pdb=" O   VAL A 499 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 568 through 571
      removed outlier: 5.246A  pdb=" N   LEU A 551 " --> pdb=" O   ASP A 617 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   LEU A 612 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   VAL A 650 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   VAL A 614 " --> pdb=" O   VAL A 650 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   VAL A 652 " --> pdb=" O   VAL A 614 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ARG A 616 " --> pdb=" O   VAL A 652 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL A 649 " --> pdb=" O   THR A 714 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   SER A 679 " --> pdb=" O   THR A 691 " (cutoff:3.500A)

    247 hydrogen bonds defined for protein.
    711 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2133
        1.34 -     1.46: 1305
        1.46 -     1.58: 2881
        1.58 -     1.70: 0
        1.70 -     1.81: 24
  Bond restraints: 6343
  Sorted by residual:
  bond pdb=" CA  THR A  83 "
       pdb=" C   THR A  83 "
    ideal  model  delta    sigma   weight residual
    1.522  1.501  0.022 1.23e-02 6.61e+03 3.10e+00
  bond pdb=" CA  ARG A 435 "
       pdb=" CB  ARG A 435 "
    ideal  model  delta    sigma   weight residual
    1.526  1.546 -0.021 1.68e-02 3.54e+03 1.49e+00
  bond pdb=" CA  VAL A 607 "
       pdb=" CB  VAL A 607 "
    ideal  model  delta    sigma   weight residual
    1.546  1.536  0.011 8.80e-03 1.29e+04 1.46e+00
  bond pdb=" C   THR A  83 "
       pdb=" O   THR A  83 "
    ideal  model  delta    sigma   weight residual
    1.234  1.248 -0.014 1.26e-02 6.30e+03 1.21e+00
  bond pdb=" CA  VAL A 308 "
       pdb=" CB  VAL A 308 "
    ideal  model  delta    sigma   weight residual
    1.546  1.537  0.009 8.80e-03 1.29e+04 9.86e-01
  ... (remaining 6338 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 8204
        1.38 -     2.76: 325
        2.76 -     4.14: 74
        4.14 -     5.52: 10
        5.52 -     6.90: 1
  Bond angle restraints: 8614
  Sorted by residual:
  angle pdb=" N   VAL A 317 "
        pdb=" CA  VAL A 317 "
        pdb=" C   VAL A 317 "
      ideal   model   delta    sigma   weight residual
     112.80  107.54    5.26 1.15e+00 7.56e-01 2.09e+01
  angle pdb=" C   GLY A 362 "
        pdb=" N   GLN A 363 "
        pdb=" CA  GLN A 363 "
      ideal   model   delta    sigma   weight residual
     121.72  126.48   -4.76 1.54e+00 4.22e-01 9.54e+00
  angle pdb=" C   ILE A 586 "
        pdb=" N   ASP A 587 "
        pdb=" CA  ASP A 587 "
      ideal   model   delta    sigma   weight residual
     121.54  126.64   -5.10 1.91e+00 2.74e-01 7.14e+00
  angle pdb=" C   GLY A 172 "
        pdb=" N   ASP A 173 "
        pdb=" CA  ASP A 173 "
      ideal   model   delta    sigma   weight residual
     125.66  130.57   -4.91 1.85e+00 2.92e-01 7.05e+00
  angle pdb=" CA  THR A  83 "
        pdb=" C   THR A  83 "
        pdb=" O   THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.44  118.48    2.96 1.17e+00 7.31e-01 6.42e+00
  ... (remaining 8609 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.46: 3388
       16.46 -    32.91: 341
       32.91 -    49.37: 76
       49.37 -    65.83: 19
       65.83 -    82.28: 17
  Dihedral angle restraints: 3841
    sinusoidal: 1592
      harmonic: 2249
  Sorted by residual:
  dihedral pdb=" CA  THR A 296 "
           pdb=" C   THR A 296 "
           pdb=" N   THR A 297 "
           pdb=" CA  THR A 297 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.35   21.65     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  ASP A 329 "
           pdb=" CB  ASP A 329 "
           pdb=" CG  ASP A 329 "
           pdb=" OD1 ASP A 329 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.95   57.95     1      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" CA  GLU A 775 "
           pdb=" C   GLU A 775 "
           pdb=" N   PRO A 776 "
           pdb=" CA  PRO A 776 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.69   16.31     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 3838 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 726
       0.042 -    0.083: 147
       0.083 -    0.124: 73
       0.124 -    0.166: 3
       0.166 -    0.207: 2
  Chirality restraints: 951
  Sorted by residual:
  chirality pdb=" CB  ILE A 226 "
            pdb=" CA  ILE A 226 "
            pdb=" CG1 ILE A 226 "
            pdb=" CG2 ILE A 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ASP A 173 "
            pdb=" N   ASP A 173 "
            pdb=" C   ASP A 173 "
            pdb=" CB  ASP A 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.29e-01
  chirality pdb=" CA  ILE A 744 "
            pdb=" N   ILE A 744 "
            pdb=" C   ILE A 744 "
            pdb=" CB  ILE A 744 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.80e-01
  ... (remaining 948 not shown)

  Planarity restraints: 1137
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  58 "   -0.066 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO A  59 "    0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO A  59 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A  59 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 442 "    0.053 5.00e-02 4.00e+02   8.00e-02 1.02e+01
        pdb=" N   PRO A 443 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO A 443 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 443 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 695 "    0.041 5.00e-02 4.00e+02   6.24e-02 6.24e+00
        pdb=" N   PRO A 696 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 696 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 696 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1134 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 975
        2.77 -     3.30: 5720
        3.30 -     3.83: 9531
        3.83 -     4.37: 11223
        4.37 -     4.90: 19756
  Nonbonded interactions: 47205
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 236 "
            pdb=" O   ALA A 272 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OH  TYR A 135 "
            pdb=" OD2 ASP A 326 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG1 THR A 239 "
            pdb=" OE1 GLN A 242 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" NH1 ARG A 712 "
            pdb=" O   ILE A 713 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OD2 ASP A 550 "
            pdb=" OG  SER A 755 "
     model   vdw
     2.294 3.040
  ... (remaining 47200 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:             1.170
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.110
  Find NCS groups from input model:        0.030
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6343  Z= 0.147
  Angle     :  0.653   6.903   8614  Z= 0.379
  Chirality :  0.042   0.207    951
  Planarity :  0.006   0.100   1137
  Dihedral  : 15.281  82.282   2391
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.15 %
    Favored  : 99.70 %
  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: -1.07 (0.30), residues: 777
  helix:  1.28 (0.38), residues: 200
  sheet: -1.12 (0.38), residues: 189
  loop : -1.57 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 698 
 TYR   0.015   0.001   TYR A 484 
 PHE   0.009   0.001   PHE A 469 
 TRP   0.013   0.001   TRP A 136 
 HIS   0.005   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6343)
  covalent geometry    : angle       0.65333 ( 8614)
  hydrogen bonds       : bond        0.20042 (  229)
  hydrogen bonds       : angle       7.66912 (  711)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.6677 (tmt170) cc_final: 0.6356 (tmt170)
  outliers start: 1
  outliers final: 1
  residues processed: 103
  average time/residue: 0.0893
  time to fit residues: 11.8692
Evaluate side-chains
  85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    0.0470
   overall best weight:    2.4086

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.165097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.121266 restraints weight = 7171.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.60
r_work: 0.2966 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   6343  Z= 0.250
  Angle     :  0.673   7.953   8614  Z= 0.349
  Chirality :  0.047   0.183    951
  Planarity :  0.006   0.069   1137
  Dihedral  :  5.031  36.399    872
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  8.38 %
    Favored  : 90.72 %
  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: -1.10 (0.30), residues: 777
  helix:  1.08 (0.37), residues: 210
  sheet: -0.87 (0.38), residues: 184
  loop : -1.72 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 712 
 TYR   0.017   0.002   TYR A 377 
 PHE   0.015   0.002   PHE A 232 
 TRP   0.016   0.001   TRP A 136 
 HIS   0.015   0.002   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00620 ( 6343)
  covalent geometry    : angle       0.67304 ( 8614)
  hydrogen bonds       : bond        0.05034 (  229)
  hydrogen bonds       : angle       5.56823 (  711)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.6931 (tmt170) cc_final: 0.6567 (tmt170)
REVERT: A  484 TYR cc_start: 0.8237 (t80) cc_final: 0.7932 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 87
  average time/residue: 0.0837
  time to fit residues: 9.6458
Evaluate side-chains
  79 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  771 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0770
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.169616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.119772 restraints weight = 7026.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.66
r_work: 0.3164 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6343  Z= 0.111
  Angle     :  0.546   6.943   8614  Z= 0.280
  Chirality :  0.043   0.181    951
  Planarity :  0.005   0.059   1137
  Dihedral  :  4.611  32.643    872
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.93 %
    Favored  : 87.87 %
  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 (0.30), residues: 777
  helix:  1.33 (0.37), residues: 210
  sheet: -0.58 (0.38), residues: 186
  loop : -1.58 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 712 
 TYR   0.013   0.001   TYR A 484 
 PHE   0.008   0.001   PHE A 232 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6343)
  covalent geometry    : angle       0.54567 ( 8614)
  hydrogen bonds       : bond        0.03417 (  229)
  hydrogen bonds       : angle       5.06503 (  711)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8221 (tm-30)
REVERT: A  113 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7917 (mm)
REVERT: A  349 ARG cc_start: 0.6892 (tmt170) cc_final: 0.6610 (tmt170)
REVERT: A  421 ARG cc_start: 0.7650 (tpp80) cc_final: 0.7112 (mmt90)
REVERT: A  484 TYR cc_start: 0.8251 (t80) cc_final: 0.7915 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 87
  average time/residue: 0.0934
  time to fit residues: 10.4613
Evaluate side-chains
  80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  771 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.165349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.115221 restraints weight = 7102.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.64
r_work: 0.3136 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   6343  Z= 0.224
  Angle     :  0.628   7.067   8614  Z= 0.323
  Chirality :  0.046   0.171    951
  Planarity :  0.006   0.064   1137
  Dihedral  :  4.912  32.811    872
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.02 %
    Favored  : 85.33 %
  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: -0.96 (0.30), residues: 777
  helix:  1.16 (0.37), residues: 210
  sheet: -0.63 (0.38), residues: 186
  loop : -1.71 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 660 
 TYR   0.014   0.002   TYR A 377 
 PHE   0.014   0.002   PHE A 232 
 TRP   0.013   0.001   TRP A 136 
 HIS   0.013   0.002   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 6343)
  covalent geometry    : angle       0.62850 ( 8614)
  hydrogen bonds       : bond        0.04557 (  229)
  hydrogen bonds       : angle       5.13295 (  711)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8270 (tm-30)
REVERT: A  349 ARG cc_start: 0.6905 (tmt170) cc_final: 0.6699 (tmt170)
REVERT: A  363 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7406 (mt0)
REVERT: A  417 LYS cc_start: 0.8414 (mmmm) cc_final: 0.8104 (mmmt)
REVERT: A  421 ARG cc_start: 0.7773 (tpp80) cc_final: 0.7472 (mmt90)
  outliers start: 11
  outliers final: 8
  residues processed: 86
  average time/residue: 0.0902
  time to fit residues: 9.9678
Evaluate side-chains
  84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  700 ASP
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  774 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 21 optimal weight:    0.1980
   chunk 44 optimal weight:    9.9990
   chunk 73 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.169677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.119642 restraints weight = 7163.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.67
r_work: 0.3194 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6343  Z= 0.108
  Angle     :  0.526   6.116   8614  Z= 0.271
  Chirality :  0.043   0.207    951
  Planarity :  0.005   0.056   1137
  Dihedral  :  4.499  29.065    872
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 14.37 %
    Favored  : 84.28 %
  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: -0.68 (0.30), residues: 777
  helix:  1.27 (0.37), residues: 210
  sheet: -0.41 (0.39), residues: 184
  loop : -1.48 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 712 
 TYR   0.011   0.001   TYR A 377 
 PHE   0.008   0.001   PHE A 232 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6343)
  covalent geometry    : angle       0.52559 ( 8614)
  hydrogen bonds       : bond        0.03092 (  229)
  hydrogen bonds       : angle       4.83172 (  711)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: A  349 ARG cc_start: 0.6996 (tmt170) cc_final: 0.6764 (tmt170)
REVERT: A  421 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7276 (mmt90)
  outliers start: 9
  outliers final: 7
  residues processed: 86
  average time/residue: 0.0903
  time to fit residues: 10.1291
Evaluate side-chains
  83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  700 ASP
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  774 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.166506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.122201 restraints weight = 7103.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.69
r_work: 0.2979 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   6343  Z= 0.186
  Angle     :  0.586   6.687   8614  Z= 0.301
  Chirality :  0.045   0.185    951
  Planarity :  0.005   0.059   1137
  Dihedral  :  4.689  29.518    872
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.67 %
    Favored  : 83.53 %
  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: -0.74 (0.30), residues: 777
  helix:  1.21 (0.37), residues: 210
  sheet: -0.46 (0.39), residues: 186
  loop : -1.49 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 712 
 TYR   0.013   0.002   TYR A 377 
 PHE   0.013   0.001   PHE A 232 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.012   0.002   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 6343)
  covalent geometry    : angle       0.58616 ( 8614)
  hydrogen bonds       : bond        0.03972 (  229)
  hydrogen bonds       : angle       4.95016 (  711)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: A  363 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7383 (mt0)
REVERT: A  421 ARG cc_start: 0.7731 (tpp80) cc_final: 0.7329 (mmt90)
  outliers start: 12
  outliers final: 10
  residues processed: 83
  average time/residue: 0.0809
  time to fit residues: 8.9484
Evaluate side-chains
  82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  700 ASP
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  774 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 39 optimal weight:    0.0770
   chunk 35 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.170410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.119655 restraints weight = 7127.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.71
r_work: 0.3194 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6343  Z= 0.107
  Angle     :  0.526   6.716   8614  Z= 0.271
  Chirality :  0.043   0.212    951
  Planarity :  0.005   0.054   1137
  Dihedral  :  4.379  26.641    872
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.92 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.27 %
    Favored  : 82.93 %
  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: -0.55 (0.31), residues: 777
  helix:  1.39 (0.37), residues: 210
  sheet: -0.32 (0.39), residues: 186
  loop : -1.42 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 712 
 TYR   0.011   0.001   TYR A 377 
 PHE   0.008   0.001   PHE A 232 
 TRP   0.012   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6343)
  covalent geometry    : angle       0.52625 ( 8614)
  hydrogen bonds       : bond        0.03038 (  229)
  hydrogen bonds       : angle       4.73258 (  711)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   41 ARG cc_start: 0.7747 (mmm160) cc_final: 0.7436 (mmm160)
REVERT: A   52 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8305 (tm-30)
REVERT: A  363 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7484 (mt0)
REVERT: A  421 ARG cc_start: 0.7689 (tpp80) cc_final: 0.7268 (mmt90)
  outliers start: 12
  outliers final: 9
  residues processed: 86
  average time/residue: 0.0806
  time to fit residues: 9.1812
Evaluate side-chains
  82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  700 ASP
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  774 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 32 optimal weight:    0.1980
   chunk 55 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0470
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.8280

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.168300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.124564 restraints weight = 7164.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.78
r_work: 0.3157 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6343  Z= 0.117
  Angle     :  0.540   8.180   8614  Z= 0.277
  Chirality :  0.043   0.213    951
  Planarity :  0.005   0.055   1137
  Dihedral  :  4.353  25.199    872
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.56 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.17 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.31), residues: 777
  helix:  1.44 (0.37), residues: 210
  sheet: -0.07 (0.39), residues: 195
  loop : -1.34 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 261 
 TYR   0.012   0.001   TYR A 377 
 PHE   0.009   0.001   PHE A 232 
 TRP   0.010   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6343)
  covalent geometry    : angle       0.54027 ( 8614)
  hydrogen bonds       : bond        0.03139 (  229)
  hydrogen bonds       : angle       4.70071 (  711)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: A  363 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7427 (mt0)
REVERT: A  421 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7304 (mmt90)
REVERT: A  501 GLU cc_start: 0.8069 (tt0) cc_final: 0.7784 (tt0)
REVERT: A  572 GLN cc_start: 0.8076 (mt0) cc_final: 0.7779 (mt0)
  outliers start: 11
  outliers final: 9
  residues processed: 85
  average time/residue: 0.0786
  time to fit residues: 8.8497
Evaluate side-chains
  80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  700 ASP
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  774 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   chunk 47 optimal weight:    0.0570
   chunk 76 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.0902

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.168743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.124878 restraints weight = 7153.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.50
r_work: 0.3056 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6343  Z= 0.134
  Angle     :  0.558   9.185   8614  Z= 0.287
  Chirality :  0.043   0.206    951
  Planarity :  0.005   0.056   1137
  Dihedral  :  4.384  24.664    872
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.31 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.32 %
    Favored  : 82.04 %
  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: -0.43 (0.31), residues: 777
  helix:  1.43 (0.37), residues: 210
  sheet: -0.19 (0.38), residues: 201
  loop : -1.38 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 261 
 TYR   0.012   0.001   TYR A 377 
 PHE   0.010   0.001   PHE A 232 
 TRP   0.009   0.001   TRP A 136 
 HIS   0.009   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6343)
  covalent geometry    : angle       0.55756 ( 8614)
  hydrogen bonds       : bond        0.03316 (  229)
  hydrogen bonds       : angle       4.72453 (  711)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8309 (tm-30)
REVERT: A  363 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7381 (mt0)
REVERT: A  421 ARG cc_start: 0.7661 (tpp80) cc_final: 0.6753 (mmt90)
REVERT: A  501 GLU cc_start: 0.8066 (tt0) cc_final: 0.7858 (tt0)
REVERT: A  572 GLN cc_start: 0.8099 (mt0) cc_final: 0.7777 (mt0)
REVERT: A  643 LYS cc_start: 0.8618 (tppt) cc_final: 0.8346 (tppt)
  outliers start: 11
  outliers final: 9
  residues processed: 81
  average time/residue: 0.0794
  time to fit residues: 8.6840
Evaluate side-chains
  80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  700 ASP
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  774 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 57 optimal weight:    0.1980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.169069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.119331 restraints weight = 7111.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.67
r_work: 0.3189 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6343  Z= 0.125
  Angle     :  0.546   8.966   8614  Z= 0.280
  Chirality :  0.043   0.203    951
  Planarity :  0.005   0.056   1137
  Dihedral  :  4.329  24.058    872
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.18 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.77 %
    Favored  : 81.74 %
  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: -0.35 (0.31), residues: 777
  helix:  1.49 (0.37), residues: 209
  sheet: -0.06 (0.40), residues: 193
  loop : -1.34 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 261 
 TYR   0.012   0.001   TYR A 377 
 PHE   0.009   0.001   PHE A 232 
 TRP   0.010   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6343)
  covalent geometry    : angle       0.54649 ( 8614)
  hydrogen bonds       : bond        0.03202 (  229)
  hydrogen bonds       : angle       4.69741 (  711)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8311 (tm-30)
REVERT: A  363 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7367 (mt0)
REVERT: A  421 ARG cc_start: 0.7665 (tpp80) cc_final: 0.6726 (mmt90)
REVERT: A  572 GLN cc_start: 0.8095 (mt0) cc_final: 0.7759 (mt0)
  outliers start: 10
  outliers final: 9
  residues processed: 80
  average time/residue: 0.0836
  time to fit residues: 8.8891
Evaluate side-chains
  80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  363 GLN
Chi-restraints excluded: chain A residue  551 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  700 ASP
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  774 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0870
   chunk 23 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.3964

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

Flipped N/Q/H residues before XYZ refinement:
** A  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.167726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.126120 restraints weight = 7122.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.84
r_work: 0.3026 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6343  Z= 0.158
  Angle     :  0.580   8.972   8614  Z= 0.298
  Chirality :  0.044   0.201    951
  Planarity :  0.005   0.058   1137
  Dihedral  :  4.475  25.214    872
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.44 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.77 %
    Favored  : 81.74 %
  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: -0.53 (0.31), residues: 777
  helix:  1.40 (0.36), residues: 209
  sheet: -0.33 (0.39), residues: 194
  loop : -1.40 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 261 
 TYR   0.012   0.001   TYR A 377 
 PHE   0.012   0.001   PHE A 232 
 TRP   0.009   0.001   TRP A 136 
 HIS   0.010   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6343)
  covalent geometry    : angle       0.58023 ( 8614)
  hydrogen bonds       : bond        0.03623 (  229)
  hydrogen bonds       : angle       4.79063 (  711)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1404.93 seconds
wall clock time: 24 minutes 47.50 seconds (1487.50 seconds total)