Starting phenix.real_space_refine
on Wed Mar  4 02:38:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uzs_26917/03_2026/7uzs_26917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uzs_26917/03_2026/7uzs_26917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uzs_26917/03_2026/7uzs_26917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uzs_26917/03_2026/7uzs_26917.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uzs_26917/03_2026/7uzs_26917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uzs_26917/03_2026/7uzs_26917.map"
  }
  resolution = 2.2
  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=   0.001 sd=   0.327
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    3282      2.51       5
     N     916      2.21       5
     O    1146      1.98       5
     H    5183      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10550
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "X"
      Number of atoms: 10357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 658, 10357
          Classifications: {'peptide': 658}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 627}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "X"
      Number of atoms: 193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 193
          Classifications: {'water': 193}
          Link IDs: {None: 192}
  Time building chain proxies: 2.19, per 1000 atoms: 0.21
  Number of scatterers: 10550
  At special positions: 0
  Unit cell: (97.11, 103.335, 73.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     O    1146      8.00
     N     916      7.00
     C    3282      6.00
     H    5183      1.00
    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: 0.89
  Conformation dependent library (CDL) restraints added in 338.2 milliseconds
  

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1234

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 10 sheets defined
      21.1% alpha, 37.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'X' and resid 13 through 21
    Processing helix  chain 'X' and resid 51 through 58
    Processing helix  chain 'X' and resid 151 through 159
    Processing helix  chain 'X' and resid 187 through 197
    Processing helix  chain 'X' and resid 201 through 206
      removed outlier: 3.755A  pdb=" N   SER X 206 " --> pdb=" O   GLU X 203 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 207 through 227
    Processing helix  chain 'X' and resid 247 through 258
      removed outlier: 4.194A  pdb=" N   ILE X 251 " --> pdb=" O   GLY X 247 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 264 through 268
    Processing helix  chain 'X' and resid 269 through 282
      removed outlier: 4.063A  pdb=" N   ALA X 273 " --> pdb=" O   TRP X 269 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 368 through 374
    Processing helix  chain 'X' and resid 381 through 389
      removed outlier: 3.597A  pdb=" N   ILE X 389 " --> pdb=" O   LEU X 385 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 431 through 436
      removed outlier: 3.899A  pdb=" N   TYR X 435 " --> pdb=" O   ILE X 431 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 441 through 459
    Processing helix  chain 'X' and resid 550 through 552
      No H-bonds generated for 'chain 'X' and resid 550 through 552'
    Processing sheet with id=AA1, first strand: chain 'X' and resid 7 through 11
      removed outlier: 6.539A  pdb=" N   SER X 101 " --> pdb=" O   ARG X  97 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ARG X  97 " --> pdb=" O   SER X 101 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   THR X 103 " --> pdb=" O   GLU X  95 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'X' and resid 32 through 34
      removed outlier: 6.828A  pdb=" N   LEU X 119 " --> pdb=" O   LEU X 131 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   GLN X 133 " --> pdb=" O   TYR X 117 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   TYR X 117 " --> pdb=" O   GLN X 133 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   THR X 135 " --> pdb=" O   GLY X 115 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   GLY X 115 " --> pdb=" O   THR X 135 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'X' and resid 163 through 170
    Processing sheet with id=AA4, first strand: chain 'X' and resid 362 through 367
      removed outlier: 4.060A  pdb=" N   SER X 362 " --> pdb=" O   SER X 352 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   THR X 330 " --> pdb=" O   LEU X 349 " (cutoff:3.500A)
      removed outlier: 11.835A  pdb=" N   THR X 328 " --> pdb=" O   PRO X 351 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ILE X 323 " --> pdb=" O   ALA X 295 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ALA X 295 " --> pdb=" O   ILE X 323 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ILE X 325 " --> pdb=" O   ALA X 293 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   VAL X 288 " --> pdb=" O   THR X 420 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   THR X 420 " --> pdb=" O   VAL X 288 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   THR X 290 " --> pdb=" O   ILE X 418 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ILE X 418 " --> pdb=" O   THR X 290 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'X' and resid 303 through 309
      removed outlier: 5.974A  pdb=" N   ILE X 304 " --> pdb=" O   VAL X 394 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   TRP X 396 " --> pdb=" O   ILE X 304 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   GLU X 306 " --> pdb=" O   TRP X 396 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   CYS X 398 " --> pdb=" O   GLU X 306 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   TYR X 308 " --> pdb=" O   CYS X 398 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'X' and resid 408 through 409
      removed outlier: 6.352A  pdb=" N   ASP X 408 " --> pdb=" O   PHE X 578 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   GLN X 580 " --> pdb=" O   ASP X 408 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'X' and resid 408 through 409
      removed outlier: 6.352A  pdb=" N   ASP X 408 " --> pdb=" O   PHE X 578 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   GLN X 580 " --> pdb=" O   ASP X 408 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   ILE X 585 " --> pdb=" O   THR X 560 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   THR X 560 " --> pdb=" O   ILE X 585 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LYS X 505 " --> pdb=" O   LEU X 533 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU X 533 " --> pdb=" O   LYS X 505 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   VAL X 507 " --> pdb=" O   LEU X 531 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LEU X 531 " --> pdb=" O   VAL X 507 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   LEU X 509 " --> pdb=" O   LYS X 529 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LYS X 529 " --> pdb=" O   LEU X 509 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ILE X 511 " --> pdb=" O   TRP X 527 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   TRP X 527 " --> pdb=" O   ILE X 511 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   VAL X 513 " --> pdb=" O   LYS X 525 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   LYS X 525 " --> pdb=" O   VAL X 513 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ALA X 515 " --> pdb=" O   ALA X 523 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'X' and resid 475 through 480
    Processing sheet with id=AA9, first strand: chain 'X' and resid 590 through 593
    Processing sheet with id=AB1, first strand: chain 'X' and resid 597 through 599
      removed outlier: 6.437A  pdb=" N   ALA X 598 " --> pdb=" O   VAL X 685 " (cutoff:3.500A)

    209 hydrogen bonds defined for protein.
    585 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: 2.26

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5168
        1.03 -     1.23: 73
        1.23 -     1.42: 2129
        1.42 -     1.62: 3063
        1.62 -     1.81: 31
  Bond restraints: 10464
  Sorted by residual:
  bond pdb=" N   ILE X 284 "
       pdb=" CA  ILE X 284 "
    ideal  model  delta    sigma   weight residual
    1.460  1.491 -0.031 7.30e-03 1.88e+04 1.75e+01
  bond pdb=" N   ILE X 431 "
       pdb=" CA  ILE X 431 "
    ideal  model  delta    sigma   weight residual
    1.455  1.493 -0.038 1.04e-02 9.25e+03 1.35e+01
  bond pdb=" C   VAL X 288 "
       pdb=" O   VAL X 288 "
    ideal  model  delta    sigma   weight residual
    1.238  1.200  0.037 1.17e-02 7.31e+03 1.02e+01
  bond pdb=" C   PRO X 285 "
       pdb=" O   PRO X 285 "
    ideal  model  delta    sigma   weight residual
    1.233  1.196  0.038 1.23e-02 6.61e+03 9.34e+00
  bond pdb=" C   PRO X 367 "
       pdb=" O   PRO X 367 "
    ideal  model  delta    sigma   weight residual
    1.233  1.196  0.037 1.23e-02 6.61e+03 8.96e+00
  ... (remaining 10459 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 18707
        2.31 -     4.62: 201
        4.62 -     6.92: 11
        6.92 -     9.23: 0
        9.23 -    11.54: 1
  Bond angle restraints: 18920
  Sorted by residual:
  angle pdb=" N   LEU X 131 "
        pdb=" CA  LEU X 131 "
        pdb=" C   LEU X 131 "
      ideal   model   delta    sigma   weight residual
     112.90  107.59    5.31 1.31e+00 5.83e-01 1.64e+01
  angle pdb=" CA  THR X 432 "
        pdb=" C   THR X 432 "
        pdb=" O   THR X 432 "
      ideal   model   delta    sigma   weight residual
     120.63  116.26    4.37 1.08e+00 8.57e-01 1.64e+01
  angle pdb=" C   THR X 135 "
        pdb=" CA  THR X 135 "
        pdb=" CB  THR X 135 "
      ideal   model   delta    sigma   weight residual
     109.72  116.10   -6.38 1.73e+00 3.34e-01 1.36e+01
  angle pdb=" CA  PHE X 134 "
        pdb=" CB  PHE X 134 "
        pdb=" CG  PHE X 134 "
      ideal   model   delta    sigma   weight residual
     113.80  117.38   -3.58 1.00e+00 1.00e+00 1.28e+01
  angle pdb=" N   ILE X 431 "
        pdb=" CA  ILE X 431 "
        pdb=" C   ILE X 431 "
      ideal   model   delta    sigma   weight residual
     112.43  109.15    3.28 9.20e-01 1.18e+00 1.27e+01
  ... (remaining 18915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 4359
       17.89 -    35.77: 349
       35.77 -    53.66: 138
       53.66 -    71.54: 34
       71.54 -    89.43: 21
  Dihedral angle restraints: 4901
    sinusoidal: 2690
      harmonic: 2211
  Sorted by residual:
  dihedral pdb=" CB  GLU X 540 "
           pdb=" CG  GLU X 540 "
           pdb=" CD  GLU X 540 "
           pdb=" OE1 GLU X 540 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.43  -89.43     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU X 502 "
           pdb=" CG  GLU X 502 "
           pdb=" CD  GLU X 502 "
           pdb=" OE1 GLU X 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.66   86.66     1      3.00e+01 1.11e-03 1.00e+01
  dihedral pdb=" CB  GLU X 572 "
           pdb=" CG  GLU X 572 "
           pdb=" CD  GLU X 572 "
           pdb=" OE1 GLU X 572 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.51   86.51     1      3.00e+01 1.11e-03 1.00e+01
  ... (remaining 4898 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 507
       0.033 -    0.067: 197
       0.067 -    0.100: 47
       0.100 -    0.133: 50
       0.133 -    0.167: 10
  Chirality restraints: 811
  Sorted by residual:
  chirality pdb=" CA  LEU X  61 "
            pdb=" N   LEU X  61 "
            pdb=" C   LEU X  61 "
            pdb=" CB  LEU X  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.96e-01
  chirality pdb=" CA  ARG X 369 "
            pdb=" N   ARG X 369 "
            pdb=" C   ARG X 369 "
            pdb=" CB  ARG X 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.96e-01
  chirality pdb=" CA  VAL X 289 "
            pdb=" N   VAL X 289 "
            pdb=" C   VAL X 289 "
            pdb=" CB  VAL X 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.05e-01
  ... (remaining 808 not shown)

  Planarity restraints: 1547
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN X  64 "    0.246 2.00e-02 2.50e+03   2.92e-01 1.28e+03
        pdb=" CD  GLN X  64 "   -0.032 2.00e-02 2.50e+03
        pdb=" OE1 GLN X  64 "   -0.226 2.00e-02 2.50e+03
        pdb=" NE2 GLN X  64 "   -0.004 2.00e-02 2.50e+03
        pdb="HE21 GLN X  64 "   -0.439 2.00e-02 2.50e+03
        pdb="HE22 GLN X  64 "    0.455 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN X 133 "   -0.221 2.00e-02 2.50e+03   2.56e-01 9.81e+02
        pdb=" CD  GLN X 133 "    0.014 2.00e-02 2.50e+03
        pdb=" OE1 GLN X 133 "    0.212 2.00e-02 2.50e+03
        pdb=" NE2 GLN X 133 "    0.002 2.00e-02 2.50e+03
        pdb="HE21 GLN X 133 "    0.383 2.00e-02 2.50e+03
        pdb="HE22 GLN X 133 "   -0.390 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN X 434 "    0.130 2.00e-02 2.50e+03   1.40e-01 2.92e+02
        pdb=" CG  ASN X 434 "   -0.008 2.00e-02 2.50e+03
        pdb=" OD1 ASN X 434 "   -0.126 2.00e-02 2.50e+03
        pdb=" ND2 ASN X 434 "   -0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN X 434 "    0.208 2.00e-02 2.50e+03
        pdb="HD22 ASN X 434 "   -0.202 2.00e-02 2.50e+03
  ... (remaining 1544 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 995
        2.22 -     2.82: 22673
        2.82 -     3.41: 29308
        3.41 -     4.01: 41980
        4.01 -     4.60: 60517
  Nonbonded interactions: 155473
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP X 669 "
            pdb=" H   ASN X 675 "
     model   vdw
     1.628 2.450
  nonbonded pdb=" HE1 TRP X 179 "
            pdb=" OG  SER X 248 "
     model   vdw
     1.679 2.450
  nonbonded pdb=" O   PRO X 557 "
            pdb=" HG1 THR X 560 "
     model   vdw
     1.700 2.450
  nonbonded pdb=" HH  TYR X 518 "
            pdb=" O   HOH X 714 "
     model   vdw
     1.701 2.450
  nonbonded pdb=" HG  SER X  91 "
            pdb=" OG1 THR X 107 "
     model   vdw
     1.702 2.450
  ... (remaining 155468 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:             1.490
  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:             0.070
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.730
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:6.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
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      :  0.004   0.044   5281  Z= 0.286
  Angle     :  0.721   6.385   7166  Z= 0.441
  Chirality :  0.047   0.167    811
  Planarity :  0.005   0.106    923
  Dihedral  : 17.955  89.429   1947
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.99 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.32), residues: 650
  helix:  1.50 (0.49), residues: 117
  sheet:  0.52 (0.31), residues: 248
  loop :  0.79 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG X 320 
 TYR   0.014   0.002   TYR X 167 
 PHE   0.020   0.002   PHE X 134 
 TRP   0.009   0.001   TRP X 333 
 HIS   0.008   0.001   HIS X 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 5281)
  covalent geometry    : angle       0.72073 ( 7166)
  hydrogen bonds       : bond        0.10378 (  209)
  hydrogen bonds       : angle       6.78601 (  585)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  230 is missing expected H atoms. Skipping.
Residue SER  352 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X  599 GLU cc_start: 0.8204 (tt0) cc_final: 0.7913 (tt0)
  outliers start: 10
  outliers final: 4
  residues processed: 108
  average time/residue: 1.7539
  time to fit residues: 195.4037
Evaluate side-chains
  98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  403 THR
Chi-restraints excluded: chain X residue  407 THR
Chi-restraints excluded: chain X residue  505 LYS
Chi-restraints excluded: chain X residue  572 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 64 optimal weight:    7.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
X  68 GLN
X 175 GLN
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 646 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.128005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.107812 restraints weight = 13334.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 1.05
r_work: 0.3019 rms_B_bonded: 1.19 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.0635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5281  Z= 0.152
  Angle     :  0.537   5.271   7166  Z= 0.284
  Chirality :  0.042   0.155    811
  Planarity :  0.004   0.035    923
  Dihedral  :  6.342  77.495    721
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 14.49 %
    Favored  : 82.29 %
  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:  1.28 (0.32), residues: 650
  helix:  1.99 (0.47), residues: 118
  sheet:  0.63 (0.31), residues: 248
  loop :  0.74 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X 155 
 TYR   0.017   0.002   TYR X 167 
 PHE   0.013   0.002   PHE X 639 
 TRP   0.005   0.001   TRP X 333 
 HIS   0.004   0.001   HIS X 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 5281)
  covalent geometry    : angle       0.53744 ( 7166)
  hydrogen bonds       : bond        0.04220 (  209)
  hydrogen bonds       : angle       5.71055 (  585)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  230 is missing expected H atoms. Skipping.
Residue SER  352 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X  442 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8129 (mp)
REVERT: X  611 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7194 (tm-30)
  outliers start: 18
  outliers final: 5
  residues processed: 107
  average time/residue: 1.7470
  time to fit residues: 192.6016
Evaluate side-chains
  102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  403 THR
Chi-restraints excluded: chain X residue  407 THR
Chi-restraints excluded: chain X residue  442 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  611 GLN
Chi-restraints excluded: chain X residue  620 ASP
Chi-restraints excluded: chain X residue  649 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 63 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
X  68 GLN
X 175 GLN
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 646 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.125555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.105196 restraints weight = 13471.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 1.05
r_work: 0.2983 rms_B_bonded: 1.19 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5281  Z= 0.222
  Angle     :  0.599   5.367   7166  Z= 0.320
  Chirality :  0.043   0.162    811
  Planarity :  0.005   0.040    923
  Dihedral  :  5.280  31.075    714
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.31 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.31), residues: 650
  helix:  1.88 (0.47), residues: 118
  sheet:  0.64 (0.30), residues: 246
  loop :  0.41 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG X 450 
 TYR   0.022   0.003   TYR X 167 
 PHE   0.021   0.002   PHE X 639 
 TRP   0.007   0.001   TRP X 643 
 HIS   0.007   0.002   HIS X 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 5281)
  covalent geometry    : angle       0.59948 ( 7166)
  hydrogen bonds       : bond        0.04846 (  209)
  hydrogen bonds       : angle       5.89635 (  585)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  230 is missing expected H atoms. Skipping.
Residue SER  352 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X  442 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8196 (mp)
REVERT: X  611 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7623 (tm-30)
  outliers start: 17
  outliers final: 6
  residues processed: 110
  average time/residue: 1.7028
  time to fit residues: 193.0156
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 SER
Chi-restraints excluded: chain X residue  403 THR
Chi-restraints excluded: chain X residue  442 LEU
Chi-restraints excluded: chain X residue  530 LYS
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  611 GLN
Chi-restraints excluded: chain X residue  620 ASP
Chi-restraints excluded: chain X residue  649 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 62 optimal weight:    0.1980
   overall best weight:    2.6388

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

Flipped N/Q/H residues before XYZ refinement:
X 128 GLN
X 175 GLN
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 646 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.127877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.107698 restraints weight = 13396.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 1.05
r_work: 0.2997 rms_B_bonded: 1.18 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.0944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5281  Z= 0.150
  Angle     :  0.532   5.177   7166  Z= 0.281
  Chirality :  0.042   0.155    811
  Planarity :  0.004   0.039    923
  Dihedral  :  4.953  27.572    713
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.74 %
    Favored  : 81.57 %
  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:  1.15 (0.32), residues: 650
  helix:  2.09 (0.47), residues: 118
  sheet:  0.55 (0.31), residues: 252
  loop :  0.55 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X 155 
 TYR   0.017   0.002   TYR X 167 
 PHE   0.015   0.002   PHE X 639 
 TRP   0.005   0.001   TRP X 333 
 HIS   0.003   0.001   HIS X 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5281)
  covalent geometry    : angle       0.53153 ( 7166)
  hydrogen bonds       : bond        0.04046 (  209)
  hydrogen bonds       : angle       5.63815 (  585)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  230 is missing expected H atoms. Skipping.
Residue SER  352 is missing expected H atoms. Skipping.
Evaluate side-chains
  118 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.291 
Fit side-chains
REVERT: X  400 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5527 (mp0)
REVERT: X  442 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8154 (mp)
REVERT: X  611 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7582 (tm-30)
  outliers start: 15
  outliers final: 7
  residues processed: 112
  average time/residue: 1.7540
  time to fit residues: 202.3367
Evaluate side-chains
  112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 SER
Chi-restraints excluded: chain X residue  310 GLU
Chi-restraints excluded: chain X residue  400 GLU
Chi-restraints excluded: chain X residue  403 THR
Chi-restraints excluded: chain X residue  442 LEU
Chi-restraints excluded: chain X residue  533 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  611 GLN
Chi-restraints excluded: chain X residue  620 ASP
Chi-restraints excluded: chain X residue  649 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 47 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
X 175 GLN
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 646 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.126061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.105845 restraints weight = 13298.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 1.04
r_work: 0.2994 rms_B_bonded: 1.18 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.1029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5281  Z= 0.213
  Angle     :  0.585   5.603   7166  Z= 0.311
  Chirality :  0.043   0.158    811
  Planarity :  0.005   0.041    923
  Dihedral  :  5.164  25.838    713
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.38 %
    Favored  : 81.75 %
  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:  0.97 (0.32), residues: 650
  helix:  1.90 (0.47), residues: 118
  sheet:  0.51 (0.31), residues: 251
  loop :  0.38 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG X 450 
 TYR   0.021   0.003   TYR X 167 
 PHE   0.019   0.002   PHE X 639 
 TRP   0.006   0.001   TRP X 333 
 HIS   0.005   0.002   HIS X 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 5281)
  covalent geometry    : angle       0.58515 ( 7166)
  hydrogen bonds       : bond        0.04623 (  209)
  hydrogen bonds       : angle       5.83295 (  585)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  230 is missing expected H atoms. Skipping.
Residue SER  352 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.274 
Fit side-chains
REVERT: X  400 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5528 (mp0)
REVERT: X  442 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8178 (mp)
REVERT: X  611 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7644 (tm-30)
  outliers start: 16
  outliers final: 6
  residues processed: 112
  average time/residue: 1.7425
  time to fit residues: 200.7208
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 SER
Chi-restraints excluded: chain X residue  310 GLU
Chi-restraints excluded: chain X residue  400 GLU
Chi-restraints excluded: chain X residue  442 LEU
Chi-restraints excluded: chain X residue  533 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  611 GLN
Chi-restraints excluded: chain X residue  620 ASP
Chi-restraints excluded: chain X residue  649 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
X  68 GLN
X 175 GLN
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 646 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.128139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.107908 restraints weight = 13381.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.05
r_work: 0.3015 rms_B_bonded: 1.20 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.1020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5281  Z= 0.133
  Angle     :  0.524   5.101   7166  Z= 0.275
  Chirality :  0.041   0.151    811
  Planarity :  0.004   0.040    923
  Dihedral  :  4.775  16.830    712
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 16.28 %
    Favored  : 81.40 %
  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:  1.15 (0.32), residues: 650
  helix:  2.17 (0.47), residues: 118
  sheet:  0.54 (0.31), residues: 251
  loop :  0.52 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X  46 
 TYR   0.016   0.002   TYR X 167 
 PHE   0.013   0.002   PHE X 639 
 TRP   0.004   0.001   TRP X 333 
 HIS   0.003   0.001   HIS X 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5281)
  covalent geometry    : angle       0.52438 ( 7166)
  hydrogen bonds       : bond        0.03828 (  209)
  hydrogen bonds       : angle       5.55790 (  585)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  230 is missing expected H atoms. Skipping.
Residue SER  352 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: X  442 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8143 (mp)
REVERT: X  611 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7571 (tm-30)
REVERT: X  649 CYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7191 (m)
  outliers start: 13
  outliers final: 3
  residues processed: 111
  average time/residue: 1.6017
  time to fit residues: 183.3552
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 SER
Chi-restraints excluded: chain X residue  442 LEU
Chi-restraints excluded: chain X residue  533 LEU
Chi-restraints excluded: chain X residue  534 THR
Chi-restraints excluded: chain X residue  611 GLN
Chi-restraints excluded: chain X residue  649 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
X  68 GLN
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 646 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.130409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.110300 restraints weight = 13458.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.05
r_work: 0.3055 rms_B_bonded: 1.21 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 2.05 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.1080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5281  Z= 0.094
  Angle     :  0.488   5.408   7166  Z= 0.252
  Chirality :  0.041   0.144    811
  Planarity :  0.003   0.039    923
  Dihedral  :  4.429  15.694    712
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.17 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.33), residues: 650
  helix:  2.36 (0.48), residues: 118
  sheet:  0.61 (0.31), residues: 252
  loop :  0.73 (0.39), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X  46 
 TYR   0.012   0.001   TYR X 167 
 PHE   0.008   0.001   PHE X 639 
 TRP   0.004   0.000   TRP X  90 
 HIS   0.002   0.001   HIS X 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 5281)
  covalent geometry    : angle       0.48783 ( 7166)
  hydrogen bonds       : bond        0.03151 (  209)
  hydrogen bonds       : angle       5.21455 (  585)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  230 is missing expected H atoms. Skipping.
Residue SER  352 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X  442 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8059 (mp)
REVERT: X  649 CYS cc_start: 0.7599 (t) cc_final: 0.7162 (m)
  outliers start: 9
  outliers final: 4
  residues processed: 107
  average time/residue: 1.7036
  time to fit residues: 188.0218
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 SER
Chi-restraints excluded: chain X residue  407 THR
Chi-restraints excluded: chain X residue  442 LEU
Chi-restraints excluded: chain X residue  530 LYS
Chi-restraints excluded: chain X residue  534 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 19 optimal weight:    0.4980
   chunk 8 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
X  68 GLN
X 175 GLN
X 225 GLN
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 646 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.131387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.111530 restraints weight = 13433.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 1.04
r_work: 0.3063 rms_B_bonded: 1.20 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 2.04 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5281  Z= 0.097
  Angle     :  0.489   5.339   7166  Z= 0.251
  Chirality :  0.041   0.143    811
  Planarity :  0.003   0.038    923
  Dihedral  :  4.334  15.365    712
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 18.07 %
    Favored  : 80.68 %
  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:  1.49 (0.33), residues: 650
  helix:  2.43 (0.49), residues: 118
  sheet:  0.77 (0.31), residues: 246
  loop :  0.73 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X  46 
 TYR   0.012   0.001   TYR X 167 
 PHE   0.010   0.001   PHE X 548 
 TRP   0.003   0.000   TRP X  90 
 HIS   0.002   0.001   HIS X 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 5281)
  covalent geometry    : angle       0.48863 ( 7166)
  hydrogen bonds       : bond        0.03151 (  209)
  hydrogen bonds       : angle       5.15863 (  585)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  230 is missing expected H atoms. Skipping.
Residue SER  352 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: X  442 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8050 (mp)
REVERT: X  649 CYS cc_start: 0.7587 (t) cc_final: 0.7153 (m)
  outliers start: 7
  outliers final: 2
  residues processed: 106
  average time/residue: 1.8076
  time to fit residues: 197.2516
Evaluate side-chains
  102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 SER
Chi-restraints excluded: chain X residue  442 LEU
Chi-restraints excluded: chain X residue  534 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
X 175 GLN
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 646 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.130255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.110121 restraints weight = 13397.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.05
r_work: 0.3047 rms_B_bonded: 1.20 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 2.04 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.1088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5281  Z= 0.112
  Angle     :  0.501   5.831   7166  Z= 0.258
  Chirality :  0.041   0.145    811
  Planarity :  0.003   0.038    923
  Dihedral  :  4.410  15.293    712
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.35 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.33), residues: 650
  helix:  2.39 (0.48), residues: 118
  sheet:  0.78 (0.31), residues: 246
  loop :  0.72 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X  46 
 TYR   0.014   0.001   TYR X 167 
 PHE   0.009   0.001   PHE X 548 
 TRP   0.003   0.001   TRP X  90 
 HIS   0.002   0.001   HIS X 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5281)
  covalent geometry    : angle       0.50141 ( 7166)
  hydrogen bonds       : bond        0.03358 (  209)
  hydrogen bonds       : angle       5.23826 (  585)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  230 is missing expected H atoms. Skipping.
Residue SER  352 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: X  442 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8066 (mp)
  outliers start: 10
  outliers final: 4
  residues processed: 104
  average time/residue: 1.7872
  time to fit residues: 191.4769
Evaluate side-chains
  100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 SER
Chi-restraints excluded: chain X residue  310 GLU
Chi-restraints excluded: chain X residue  407 THR
Chi-restraints excluded: chain X residue  442 LEU
Chi-restraints excluded: chain X residue  534 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 17 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
X  68 GLN
X 175 GLN
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 646 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.131099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.110974 restraints weight = 13429.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.05
r_work: 0.3063 rms_B_bonded: 1.21 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 2.05 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5281  Z= 0.098
  Angle     :  0.484   5.014   7166  Z= 0.249
  Chirality :  0.041   0.141    811
  Planarity :  0.003   0.039    923
  Dihedral  :  4.306  15.215    712
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 18.60 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.33), residues: 650
  helix:  2.43 (0.48), residues: 118
  sheet:  0.80 (0.31), residues: 246
  loop :  0.75 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X  46 
 TYR   0.012   0.001   TYR X 167 
 PHE   0.008   0.001   PHE X 292 
 TRP   0.004   0.000   TRP X  90 
 HIS   0.002   0.001   HIS X 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 5281)
  covalent geometry    : angle       0.48423 ( 7166)
  hydrogen bonds       : bond        0.03143 (  209)
  hydrogen bonds       : angle       5.14826 (  585)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  230 is missing expected H atoms. Skipping.
Residue SER  352 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: X  442 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8046 (mp)
  outliers start: 6
  outliers final: 3
  residues processed: 103
  average time/residue: 1.6833
  time to fit residues: 178.7121
Evaluate side-chains
  102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue  118 SER
Chi-restraints excluded: chain X residue  407 THR
Chi-restraints excluded: chain X residue  442 LEU
Chi-restraints excluded: chain X residue  534 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
X 175 GLN
** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 646 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.126772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.106364 restraints weight = 13429.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 1.05
r_work: 0.2984 rms_B_bonded: 1.19 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5281  Z= 0.206
  Angle     :  0.583   5.963   7166  Z= 0.307
  Chirality :  0.043   0.158    811
  Planarity :  0.005   0.038    923
  Dihedral  :  4.900  17.366    712
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.71 %
    Favored  : 80.68 %
  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:  1.23 (0.32), residues: 650
  helix:  2.12 (0.47), residues: 118
  sheet:  0.71 (0.31), residues: 248
  loop :  0.51 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG X 450 
 TYR   0.020   0.002   TYR X 167 
 PHE   0.013   0.002   PHE X  39 
 TRP   0.006   0.001   TRP X 179 
 HIS   0.006   0.001   HIS X 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 5281)
  covalent geometry    : angle       0.58282 ( 7166)
  hydrogen bonds       : bond        0.04407 (  209)
  hydrogen bonds       : angle       5.67699 (  585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5447.98 seconds
wall clock time: 92 minutes 40.15 seconds (5560.15 seconds total)