Starting phenix.real_space_refine
on Thu Oct 22 21:34:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wuy_66275/10_2026/9wuy_66275.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wuy_66275/10_2026/9wuy_66275.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wuy_66275/10_2026/9wuy_66275.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wuy_66275/10_2026/9wuy_66275.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wuy_66275/10_2026/9wuy_66275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wuy_66275/10_2026/9wuy_66275.map"
  }
  resolution = 3.22
  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=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 146 atoms to isotropic.
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
     Ca      1      9.91       5
     P       1      5.49       5
     S      36      5.16       5
     C    3652      2.51       5
     N     974      2.21       5
     O    1026      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5690
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2905
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 364, 2897
          Classifications: {'peptide': 364}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 340}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
      Conformer: "B"
        Number of residues, atoms: 364, 2897
          Classifications: {'peptide': 364}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 340}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
          bond proxies already assigned to first conformer: 2956
    Chain: "A"
      Number of atoms: 2783
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 347, 2776
          Classifications: {'peptide': 347}
          Link IDs: {'PTRANS': 23, 'TRANS': 323}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
      Conformer: "B"
        Number of residues, atoms: 347, 2776
          Classifications: {'peptide': 347}
          Link IDs: {'PTRANS': 23, 'TRANS': 323}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
          bond proxies already assigned to first conformer: 2836
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 2.16, per 1000 atoms: 0.38
  Number of scatterers: 5690
  At special positions: 0
  Unit cell: (70.14, 93.52, 102.204, 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)
     Ca      1     19.99
     S      36     16.00
     P       1     15.00
     O    1026      8.00
     N     974      7.00
     C    3652      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: 0.34
  Conformation dependent library (CDL) restraints added in 420.5 milliseconds
  

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1364

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      44.4% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'B' and resid 204 through 218
      removed outlier: 3.815A  pdb=" N   ILE B 210 " --> pdb=" O   ASN B 206 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU B 211 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG B 216 " --> pdb=" O   LYS B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 240
      removed outlier: 3.847A  pdb=" N   GLU B 236 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG B 240 " --> pdb=" O   GLU B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 305
    Processing helix  chain 'B' and resid 306 through 308
      No H-bonds generated for 'chain 'B' and resid 306 through 308'
    Processing helix  chain 'B' and resid 310 through 330
    Processing helix  chain 'B' and resid 390 through 395
    Processing helix  chain 'B' and resid 410 through 422
      removed outlier: 3.858A  pdb=" N   TYR B 419 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   GLU B 420 " --> pdb=" O   ALA B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 444
      removed outlier: 3.912A  pdb=" N   LEU B 444 " --> pdb=" O   GLU B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 463
    Processing helix  chain 'B' and resid 466 through 470
    Processing helix  chain 'B' and resid 472 through 486
      removed outlier: 3.749A  pdb=" N   CYS B 480 " --> pdb=" O   ALA B 476 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLN B 481 " --> pdb=" O   ALA B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 492
      removed outlier: 3.666A  pdb=" N   LYS B 492 " --> pdb=" O   THR B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 517
    Processing helix  chain 'B' and resid 536 through 549
      removed outlier: 3.783A  pdb=" N   ARG B 549 " --> pdb=" O   SER B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 564
    Processing helix  chain 'A' and resid 205 through 218
      removed outlier: 3.592A  pdb=" N   ILE A 210 " --> pdb=" O   ASN A 206 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LYS A 212 " --> pdb=" O   MET A 208 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA A 213 " --> pdb=" O   GLU A 209 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG A 216 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   THR A 218 " --> pdb=" O   MET A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 239
    Processing helix  chain 'A' and resid 301 through 305
    Processing helix  chain 'A' and resid 310 through 330
    Processing helix  chain 'A' and resid 390 through 395
    Processing helix  chain 'A' and resid 408 through 422
      removed outlier: 3.884A  pdb=" N   TRP A 412 " --> pdb=" O   LYS A 408 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   TYR A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   GLU A 420 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 444
      removed outlier: 3.725A  pdb=" N   LEU A 444 " --> pdb=" O   GLU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 463
      removed outlier: 3.560A  pdb=" N   LEU A 463 " --> pdb=" O   VAL A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 470
      removed outlier: 3.772A  pdb=" N   ARG A 470 " --> pdb=" O   PRO A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 486
      removed outlier: 3.973A  pdb=" N   CYS A 480 " --> pdb=" O   ALA A 476 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 484 " --> pdb=" O   CYS A 480 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA A 486 " --> pdb=" O   LEU A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 518
    Processing helix  chain 'A' and resid 536 through 549
      removed outlier: 3.677A  pdb=" N   LEU A 542 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE A 543 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG A 549 " --> pdb=" O   SER A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 565
      removed outlier: 3.641A  pdb=" N   ILE A 562 " --> pdb=" O   ALA A 558 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 194 through 199
    Processing sheet with id=AA2, first strand: chain 'B' and resid 299 through 300
      removed outlier: 3.597A  pdb=" N   ILE B 354 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 333 through 334
    Processing sheet with id=AA4, first strand: chain 'B' and resid 372 through 374
    Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 200
      removed outlier: 7.180A  pdb=" N   LYS A 295 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   ILE A 253 " --> pdb=" O   LYS A 295 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 300
    Processing sheet with id=AA7, first strand: chain 'A' and resid 334 through 335
      removed outlier: 3.665A  pdb=" N   ALA A 334 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 375

    225 hydrogen bonds defined for protein.
    638 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: 0.83

  Time building geometry restraints manager: 0.45 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: 1818
        1.34 -     1.46: 1190
        1.46 -     1.58: 2761
        1.58 -     1.69: 3
        1.69 -     1.81: 56
  Bond restraints: 5828
  Sorted by residual:
  bond pdb=" OG1 TPO B 530 "
       pdb=" P   TPO B 530 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.94e+01
  bond pdb=" O1P TPO B 530 "
       pdb=" P   TPO B 530 "
    ideal  model  delta    sigma   weight residual
    1.525  1.609 -0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" O3P TPO B 530 "
       pdb=" P   TPO B 530 "
    ideal  model  delta    sigma   weight residual
    1.528  1.609 -0.081 2.00e-02 2.50e+03 1.65e+01
  bond pdb=" O2P TPO B 530 "
       pdb=" P   TPO B 530 "
    ideal  model  delta    sigma   weight residual
    1.528  1.480  0.048 2.00e-02 2.50e+03 5.67e+00
  bond pdb=" CB  TPO A 530 "
       pdb=" OG1 TPO A 530 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.86e+00
  ... (remaining 5823 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 7865
        2.53 -     5.06: 47
        5.06 -     7.59: 7
        7.59 -    10.13: 2
       10.13 -    12.66: 1
  Bond angle restraints: 7922
  Sorted by residual:
  angle pdb=" CB  TPO B 530 "
        pdb=" OG1 TPO B 530 "
        pdb=" P   TPO B 530 "
      ideal   model   delta    sigma   weight residual
     119.31  106.65   12.66 3.00e+00 1.11e-01 1.78e+01
  angle pdb=" C   LYS A 190 "
        pdb=" N   TYR A 191 "
        pdb=" CA  TYR A 191 "
      ideal   model   delta    sigma   weight residual
     120.09  124.10   -4.01 1.25e+00 6.40e-01 1.03e+01
  angle pdb=" OG1 TPO B 530 "
        pdb=" P   TPO B 530 "
        pdb=" O1P TPO B 530 "
      ideal   model   delta    sigma   weight residual
     100.43  109.49   -9.06 3.00e+00 1.11e-01 9.12e+00
  angle pdb=" CG1 ILE B 203 "
        pdb=" CB  ILE B 203 "
        pdb=" CG2 ILE B 203 "
      ideal   model   delta    sigma   weight residual
     110.70  102.15    8.55 3.00e+00 1.11e-01 8.12e+00
  angle pdb=" C   TPO B 530 "
        pdb=" N   ARG B 531 "
        pdb=" CA  ARG B 531 "
      ideal   model   delta    sigma   weight residual
     121.70  126.82   -5.12 1.80e+00 3.09e-01 8.08e+00
  ... (remaining 7917 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3197
       17.97 -    35.93: 283
       35.93 -    53.90: 46
       53.90 -    71.86: 1
       71.86 -    89.83: 1
  Dihedral angle restraints: 3528
    sinusoidal: 1428
      harmonic: 2100
  Sorted by residual:
  dihedral pdb=" CG  ARG A 296 "
           pdb=" CD  ARG A 296 "
           pdb=" NE  ARG A 296 "
           pdb=" CZ  ARG A 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.44  -41.56     2      1.50e+01 4.44e-03 9.39e+00
  dihedral pdb=" CA  GLU A 502 "
           pdb=" CB  GLU A 502 "
           pdb=" CG  GLU A 502 "
           pdb=" CD  GLU A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  114.22  -54.22     3      1.50e+01 4.44e-03 9.27e+00
  dihedral pdb=" CG  ARG B 556 "
           pdb=" CD  ARG B 556 "
           pdb=" NE  ARG B 556 "
           pdb=" CZ  ARG B 556 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -49.64  -40.36     2      1.50e+01 4.44e-03 8.95e+00
  ... (remaining 3525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 708
       0.045 -    0.091: 144
       0.091 -    0.136: 36
       0.136 -    0.181: 0
       0.181 -    0.226: 1
  Chirality restraints: 889
  Sorted by residual:
  chirality pdb=" CB  ILE B 203 "
            pdb=" CA  ILE B 203 "
            pdb=" CG1 ILE B 203 "
            pdb=" CG2 ILE B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  TYR A 191 "
            pdb=" N   TYR A 191 "
            pdb=" C   TYR A 191 "
            pdb=" CB  TYR A 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ARG B 531 "
            pdb=" N   ARG B 531 "
            pdb=" C   ARG B 531 "
            pdb=" CB  ARG B 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.24e-01
  ... (remaining 886 not shown)

  Planarity restraints: 1005
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 492 "    0.038 5.00e-02 4.00e+02   5.86e-02 5.49e+00
        pdb=" N   PRO B 493 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 493 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 493 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 247 "    0.025 5.00e-02 4.00e+02   3.79e-02 2.29e+00
        pdb=" N   PRO B 248 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B 248 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 248 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 247 "   -0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO A 248 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 248 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 248 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1002 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 449
        2.74 -     3.28: 5294
        3.28 -     3.82: 8540
        3.82 -     4.36: 10320
        4.36 -     4.90: 18219
  Nonbonded interactions: 42822
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 531 "
            pdb=" OD1 ASN A 532 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   LEU B 515 "
            pdb=" OH  TYR A 191 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG1 THR A 499 "
            pdb=" OE1 GLU A 502 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD2 ASP A 298 "
            pdb=" OG1 THR A 347 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OD1 ASP A 359 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.282 3.040
  ... (remaining 42817 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 189 through 239 or resid 241 through 518 or resid 530 thro \ 
ugh 559 or resid 561 through 567))
  selection = (chain 'B' and (resid 189 through 239 or resid 241 through 518 or (resid 530 and \ 
 (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or  \ 
resid 531 through 559 or resid 561 through 567))
}

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:             4.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.400
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
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   0.108   5828  Z= 0.139
  Angle     :  0.519  12.656   7922  Z= 0.249
  Chirality :  0.039   0.226    889
  Planarity :  0.004   0.059   1005
  Dihedral  : 13.051  89.827   2164
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.85 (0.32), residues: 695
  helix: -0.39 (0.30), residues: 278
  sheet: -0.27 (0.57), residues: 99
  loop : -0.67 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 556 
 TYR   0.006   0.001   TYR A 191 
 PHE   0.008   0.001   PHE B 199 
 TRP   0.007   0.001   TRP B 533 
 HIS   0.001   0.000   HIS B 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.14 ( 5828)
  covalent geometry    : angle       0.51851 /  0.25 ( 7922)
  hydrogen bonds       : bond        0.27435 / 17.40 (  225)
  hydrogen bonds       : angle       7.20779 /  4.82 (  638)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.214 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0705
  time to fit residues: 6.8806
Evaluate side-chains
  60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27]
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 505 GLN
B 563 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.176273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.147556 restraints weight = 13046.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.85
r_work: 0.3306 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5828  Z= 0.146
  Angle     :  0.572   7.193   7922  Z= 0.286
  Chirality :  0.043   0.197    889
  Planarity :  0.005   0.050   1005
  Dihedral  :  3.552  12.057    772
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  5.72 %
    Favored  : 93.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.07 (0.33), residues: 695
  helix:  0.72 (0.32), residues: 285
  sheet: -0.00 (0.56), residues: 95
  loop : -0.69 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 556 
 TYR   0.014   0.002   TYR A 375 
 PHE   0.012   0.001   PHE B 291 
 TRP   0.008   0.001   TRP B 412 
 HIS   0.002   0.001   HIS A 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 ( 5828)
  covalent geometry    : angle       0.57229 /  0.29 ( 7922)
  hydrogen bonds       : bond        0.05177 /  3.44 (  225)
  hydrogen bonds       : angle       4.56934 /  2.98 (  638)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.214 
Fit side-chains
REVERT: B  230 LEU cc_start: 0.7303 (mt) cc_final: 0.6874 (mt)
  outliers start: 3
  outliers final: 3
  residues processed: 67
  average time/residue: 0.0653
  time to fit residues: 6.0087
Evaluate side-chains
  67 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [22, 6, 32, 46, 42, 7, 49, 43, 36, 60, 5]
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0670
   chunk 49 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7320

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 563 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.176567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.146405 restraints weight = 18229.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 4.25
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3621
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3621 r_free = 0.3621    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3621 r_free = 0.3621    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.3621
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5828  Z= 0.122
  Angle     :  0.535   7.009   7922  Z= 0.265
  Chirality :  0.041   0.161    889
  Planarity :  0.005   0.045   1005
  Dihedral  :  3.578  12.057    772
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  7.63 %
    Favored  : 92.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.20 (0.33), residues: 695
  helix:  1.18 (0.33), residues: 285
  sheet:  0.19 (0.56), residues: 93
  loop : -0.82 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 556 
 TYR   0.013   0.001   TYR A 375 
 PHE   0.012   0.001   PHE A 291 
 TRP   0.008   0.001   TRP B 412 
 HIS   0.003   0.001   HIS A 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.12 ( 5828)
  covalent geometry    : angle       0.53453 /  0.27 ( 7922)
  hydrogen bonds       : bond        0.04343 /  2.91 (  225)
  hydrogen bonds       : angle       4.21176 /  2.75 (  638)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.219 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 69
  average time/residue: 0.0617
  time to fit residues: 5.9627
Evaluate side-chains
  67 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [60, 13, 56, 54, 14, 55, 39, 57, 33, 21, 50]
   chunk 60 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0010
   chunk 14 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0870
   overall best weight:    0.4564

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.178025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.148456 restraints weight = 15443.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 4.81
r_work: 0.3263 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    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: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5828  Z= 0.099
  Angle     :  0.498   6.687   7922  Z= 0.250
  Chirality :  0.040   0.140    889
  Planarity :  0.004   0.040   1005
  Dihedral  :  3.488  11.790    772
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  8.11 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.33), residues: 695
  helix:  1.45 (0.33), residues: 285
  sheet:  0.10 (0.55), residues: 98
  loop : -0.78 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 556 
 TYR   0.011   0.001   TYR A 540 
 PHE   0.011   0.001   PHE A 291 
 TRP   0.008   0.001   TRP A 412 
 HIS   0.002   0.000   HIS A 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.10 ( 5828)
  covalent geometry    : angle       0.49828 /  0.25 ( 7922)
  hydrogen bonds       : bond        0.03261 /  2.17 (  225)
  hydrogen bonds       : angle       3.98182 /  2.64 (  638)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A  198 MET cc_start: 0.7782 (mmt) cc_final: 0.7543 (mmt)
  outliers start: 3
  outliers final: 2
  residues processed: 67
  average time/residue: 0.0600
  time to fit residues: 5.7411
Evaluate side-chains
  66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [26, 47, 15, 55, 4, 14, 57, 63, 21, 53, 11]
   chunk 26 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 4 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 563 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.176487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.148792 restraints weight = 17476.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 3.48
r_work: 0.3238 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3180
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3180
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5828  Z= 0.118
  Angle     :  0.515   6.367   7922  Z= 0.257
  Chirality :  0.041   0.141    889
  Planarity :  0.004   0.039   1005
  Dihedral  :  3.571  11.997    772
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.59 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.33), residues: 695
  helix:  1.48 (0.33), residues: 285
  sheet:  0.06 (0.54), residues: 98
  loop : -0.81 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 556 
 TYR   0.011   0.001   TYR A 375 
 PHE   0.011   0.001   PHE A 291 
 TRP   0.007   0.001   TRP A 412 
 HIS   0.002   0.001   HIS A 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.12 ( 5828)
  covalent geometry    : angle       0.51507 /  0.26 ( 7922)
  hydrogen bonds       : bond        0.03569 /  2.40 (  225)
  hydrogen bonds       : angle       3.94393 /  2.66 (  638)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.256 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 64
  average time/residue: 0.0621
  time to fit residues: 5.6890
Evaluate side-chains
  66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [8, 26, 32, 38, 29, 10, 69, 19, 20, 59, 28]
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.175712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.148013 restraints weight = 14334.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.73
r_work: 0.3411 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    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: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5828  Z= 0.126
  Angle     :  0.526   6.023   7922  Z= 0.261
  Chirality :  0.041   0.142    889
  Planarity :  0.004   0.040   1005
  Dihedral  :  3.677  12.656    772
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  9.22 %
    Favored  : 90.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.32 (0.33), residues: 695
  helix:  1.40 (0.33), residues: 286
  sheet: -0.00 (0.54), residues: 98
  loop : -0.82 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 556 
 TYR   0.011   0.001   TYR A 375 
 PHE   0.014   0.001   PHE A 291 
 TRP   0.007   0.001   TRP A 412 
 HIS   0.002   0.001   HIS A 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.13 ( 5828)
  covalent geometry    : angle       0.52593 /  0.26 ( 7922)
  hydrogen bonds       : bond        0.03662 /  2.47 (  225)
  hydrogen bonds       : angle       3.91416 /  2.64 (  638)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  198 MET cc_start: 0.7898 (mmt) cc_final: 0.7657 (mmt)
  outliers start: 4
  outliers final: 2
  residues processed: 68
  average time/residue: 0.0540
  time to fit residues: 5.2154
Evaluate side-chains
  64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain A residue  434 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [53, 35, 6, 16, 20, 64, 11, 68, 52, 49, 7]
   chunk 53 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0060
   chunk 64 optimal weight:    0.1980
   chunk 11 optimal weight:    0.0030
   chunk 68 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   chunk 49 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.2406

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.178985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.151768 restraints weight = 10235.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 2.17
r_work: 0.3425 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3377
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3377 r_free = 0.3377    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3377 r_free = 0.3377    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3377
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5828  Z= 0.086
  Angle     :  0.486   6.220   7922  Z= 0.242
  Chirality :  0.039   0.141    889
  Planarity :  0.004   0.039   1005
  Dihedral  :  3.446  12.168    772
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  9.86 %
    Favored  : 89.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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 (0.34), residues: 695
  helix:  1.62 (0.33), residues: 287
  sheet:  0.02 (0.54), residues: 98
  loop : -0.73 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 556 
 TYR   0.009   0.001   TYR B 540 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.008   0.001   TRP A 412 
 HIS   0.003   0.000   HIS B 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00196 /  0.09 ( 5828)
  covalent geometry    : angle       0.48558 /  0.24 ( 7922)
  hydrogen bonds       : bond        0.02646 /  1.74 (  225)
  hydrogen bonds       : angle       3.80443 /  2.60 (  638)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  210 ILE cc_start: 0.7085 (tt) cc_final: 0.6780 (mm)
  outliers start: 3
  outliers final: 1
  residues processed: 64
  average time/residue: 0.0604
  time to fit residues: 5.6759
Evaluate side-chains
  64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  559 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [54, 52, 26, 44, 4, 8, 53, 48, 12, 57, 35]
   chunk 54 optimal weight:    0.1980
   chunk 52 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 53 optimal weight:    0.4980
   chunk 48 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 563 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.177263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.148355 restraints weight = 19400.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 4.20
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3529
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3529 r_free = 0.3529    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3529 r_free = 0.3529    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3529
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5828  Z= 0.104
  Angle     :  0.497   6.035   7922  Z= 0.246
  Chirality :  0.040   0.141    889
  Planarity :  0.004   0.039   1005
  Dihedral  :  3.492  11.834    772
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 10.17 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.54 (0.34), residues: 695
  helix:  1.65 (0.33), residues: 287
  sheet: -0.09 (0.53), residues: 100
  loop : -0.70 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 556 
 TYR   0.009   0.001   TYR A 375 
 PHE   0.011   0.001   PHE A 291 
 TRP   0.007   0.001   TRP A 412 
 HIS   0.003   0.001   HIS B 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.10 ( 5828)
  covalent geometry    : angle       0.49669 /  0.25 ( 7922)
  hydrogen bonds       : bond        0.03079 /  2.06 (  225)
  hydrogen bonds       : angle       3.78614 /  2.55 (  638)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  198 MET cc_start: 0.7306 (mmt) cc_final: 0.7055 (mmt)
  outliers start: 2
  outliers final: 2
  residues processed: 63
  average time/residue: 0.0623
  time to fit residues: 5.6620
Evaluate side-chains
  65 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  559 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [0, 2, 35, 12, 28, 31, 39, 34, 27, 23, 47]
   chunk 0 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 39 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.176471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.143867 restraints weight = 15686.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 4.89
r_work: 0.3210 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3354
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3354
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5828  Z= 0.107
  Angle     :  0.502   5.903   7922  Z= 0.249
  Chirality :  0.040   0.141    889
  Planarity :  0.004   0.039   1005
  Dihedral  :  3.549  11.977    772
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 10.49 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.34), residues: 695
  helix:  1.63 (0.33), residues: 287
  sheet: -0.09 (0.54), residues: 93
  loop : -0.62 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 556 
 TYR   0.010   0.001   TYR A 375 
 PHE   0.011   0.001   PHE A 291 
 TRP   0.007   0.001   TRP A 412 
 HIS   0.002   0.001   HIS A 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.11 ( 5828)
  covalent geometry    : angle       0.50206 /  0.25 ( 7922)
  hydrogen bonds       : bond        0.03174 /  2.13 (  225)
  hydrogen bonds       : angle       3.79549 /  2.55 (  638)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.262 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 64
  average time/residue: 0.0617
  time to fit residues: 5.6317
Evaluate side-chains
  66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  559 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [66, 21, 6, 36, 33, 55, 44, 22, 39, 11, 56]
   chunk 66 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0010
   chunk 6 optimal weight:    0.7980
   chunk 36 optimal weight:    0.1980
   chunk 33 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 563 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.178351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.149824 restraints weight = 10908.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.14
r_work: 0.3396 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5828  Z= 0.090
  Angle     :  0.480   5.945   7922  Z= 0.239
  Chirality :  0.039   0.139    889
  Planarity :  0.004   0.039   1005
  Dihedral  :  3.429  11.607    772
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 10.65 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.69 (0.34), residues: 695
  helix:  1.76 (0.33), residues: 287
  sheet: -0.08 (0.54), residues: 93
  loop : -0.56 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 556 
 TYR   0.009   0.001   TYR B 540 
 PHE   0.011   0.001   PHE A 199 
 TRP   0.008   0.001   TRP A 412 
 HIS   0.002   0.000   HIS A 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.09 ( 5828)
  covalent geometry    : angle       0.47990 /  0.24 ( 7922)
  hydrogen bonds       : bond        0.02719 /  1.80 (  225)
  hydrogen bonds       : angle       3.73608 /  2.52 (  638)

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  198 MET cc_start: 0.7886 (mmt) cc_final: 0.7670 (mmt)
REVERT: A  210 ILE cc_start: 0.7150 (tt) cc_final: 0.6771 (mm)
  outliers start: 2
  outliers final: 2
  residues processed: 65
  average time/residue: 0.0574
  time to fit residues: 5.3402
Evaluate side-chains
  66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  559 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks: [12, 19, 26, 3, 65, 33, 69, 52, 41, 28, 32]
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 563 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.175335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.143041 restraints weight = 15828.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 4.42
r_work: 0.3209 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5828  Z= 0.128
  Angle     :  0.522   5.809   7922  Z= 0.258
  Chirality :  0.041   0.142    889
  Planarity :  0.004   0.039   1005
  Dihedral  :  3.629  12.312    772
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 10.65 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.54 (0.33), residues: 695
  helix:  1.61 (0.33), residues: 287
  sheet: -0.13 (0.54), residues: 93
  loop : -0.64 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 556 
 TYR   0.011   0.001   TYR A 375 
 PHE   0.012   0.001   PHE A 291 
 TRP   0.006   0.001   TRP B 412 
 HIS   0.003   0.001   HIS A 228 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.13 ( 5828)
  covalent geometry    : angle       0.52152 /  0.26 ( 7922)
  hydrogen bonds       : bond        0.03514 /  2.38 (  225)
  hydrogen bonds       : angle       3.81073 /  2.54 (  638)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1531.75 seconds
wall clock time: 26 minutes 56.51 seconds (1616.51 seconds total)