Starting phenix.real_space_refine
on Tue Mar  3 13:05:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ydq_33756/03_2026/7ydq_33756.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ydq_33756/03_2026/7ydq_33756.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ydq_33756/03_2026/7ydq_33756.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ydq_33756/03_2026/7ydq_33756.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ydq_33756/03_2026/7ydq_33756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ydq_33756/03_2026/7ydq_33756.map"
  }
  resolution = 4.04
  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=   0.003 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    3144      2.51       5
     N     760      2.21       5
     O     846      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 4778
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 598, 4753
          Classifications: {'peptide': 598}
          Link IDs: {'PTRANS': 21, 'TRANS': 576}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'IRX': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.06, per 1000 atoms: 0.22
  Number of scatterers: 4778
  At special positions: 0
  Unit cell: (84.7, 68.2, 119.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     846      8.00
     N     760      7.00
     C    3144      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: 0.30
  Conformation dependent library (CDL) restraints added in 375.1 milliseconds
  

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1112

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 1 sheets defined
      53.7% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 58
      removed outlier: 3.904A  pdb=" N   HIS A  35 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   VAL A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   TRP A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 83
      removed outlier: 3.892A  pdb=" N   ASN A  66 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   SER A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   ILE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   VAL A  79 " --> pdb=" O   CYS A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 111
      removed outlier: 3.575A  pdb=" N   PHE A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   GLN A 105 " --> pdb=" O   CYS A 101 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER A 109 " --> pdb=" O   GLN A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 145
      removed outlier: 4.119A  pdb=" N   THR A 118 " --> pdb=" O   THR A 114 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ILE A 141 " --> pdb=" O   ILE A 137 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   GLY A 142 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   SER A 143 " --> pdb=" O   PHE A 139 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   THR A 144 " --> pdb=" O   ASN A 140 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   MET A 145 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 173
      removed outlier: 3.798A  pdb=" N   GLY A 158 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   GLN A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 206
    Processing helix  chain 'A' and resid 232 through 239
      removed outlier: 3.676A  pdb=" N   SER A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 249
    Processing helix  chain 'A' and resid 249 through 257
      removed outlier: 4.273A  pdb=" N   THR A 253 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LEU A 254 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLN A 255 " --> pdb=" O   TRP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 270
    Processing helix  chain 'A' and resid 272 through 290
      removed outlier: 3.747A  pdb=" N   VAL A 276 " --> pdb=" O   SER A 272 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   THR A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   ILE A 278 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE A 279 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   VAL A 280 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLY A 281 " --> pdb=" O   THR A 277 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE A 286 " --> pdb=" O   MET A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 316
    Processing helix  chain 'A' and resid 317 through 320
    Processing helix  chain 'A' and resid 321 through 332
      removed outlier: 3.987A  pdb=" N   TRP A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ILE A 327 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 338
    Processing helix  chain 'A' and resid 339 through 355
      removed outlier: 3.900A  pdb=" N   GLN A 343 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 365
      removed outlier: 3.555A  pdb=" N   PHE A 365 " --> pdb=" O   PRO A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 379
    Processing helix  chain 'A' and resid 426 through 435
      removed outlier: 3.875A  pdb=" N   LEU A 430 " --> pdb=" O   PRO A 426 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   THR A 432 " --> pdb=" O   PRO A 428 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   THR A 433 " --> pdb=" O   THR A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.640A  pdb=" N   ASP A 452 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 461
      Proline residue:  A 459  - end of helix
    Processing helix  chain 'A' and resid 613 through 635
      removed outlier: 4.055A  pdb=" N   ILE A 617 " --> pdb=" O   LYS A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 644
    Processing sheet with id=AA1, first strand: chain 'A' and resid 382 through 392
      removed outlier: 7.326A  pdb=" N   SER A 517 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ARG A 538 " --> pdb=" O   SER A 517 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   ASN A 519 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   LYS A 536 " --> pdb=" O   ASN A 519 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   ASN A 491 " --> pdb=" O   PRO A 383 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU A 385 " --> pdb=" O   ASN A 491 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   ILE A 493 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   GLU A 387 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   LEU A 495 " --> pdb=" O   GLU A 387 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ASP A 389 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   GLY A 497 " --> pdb=" O   ASP A 389 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ASP A 391 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)

    277 hydrogen bonds defined for protein.
    768 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: 0.76

  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: 1461
        1.34 -     1.46: 1205
        1.46 -     1.58: 2184
        1.58 -     1.70: 4
        1.70 -     1.82: 43
  Bond restraints: 4897
  Sorted by residual:
  bond pdb=" C15 IRX A 701 "
       pdb=" C16 IRX A 701 "
    ideal  model  delta    sigma   weight residual
    1.482  1.633 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C10 IRX A 701 "
       pdb=" C8  IRX A 701 "
    ideal  model  delta    sigma   weight residual
    1.527  1.670 -0.143 2.00e-02 2.50e+03 5.13e+01
  bond pdb=" C18 IRX A 701 "
       pdb=" C19 IRX A 701 "
    ideal  model  delta    sigma   weight residual
    1.455  1.596 -0.141 2.00e-02 2.50e+03 4.95e+01
  bond pdb=" C7  IRX A 701 "
       pdb=" C8  IRX A 701 "
    ideal  model  delta    sigma   weight residual
    1.524  1.642 -0.118 2.00e-02 2.50e+03 3.50e+01
  bond pdb=" C11 IRX A 701 "
       pdb=" C13 IRX A 701 "
    ideal  model  delta    sigma   weight residual
    1.516  1.444  0.072 2.00e-02 2.50e+03 1.29e+01
  ... (remaining 4892 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.37: 6576
        3.37 -     6.73: 43
        6.73 -    10.10: 13
       10.10 -    13.47: 2
       13.47 -    16.83: 2
  Bond angle restraints: 6636
  Sorted by residual:
  angle pdb=" C12 IRX A 701 "
        pdb=" N4  IRX A 701 "
        pdb=" C13 IRX A 701 "
      ideal   model   delta    sigma   weight residual
     119.44  136.27  -16.83 3.00e+00 1.11e-01 3.15e+01
  angle pdb=" C10 IRX A 701 "
        pdb=" C11 IRX A 701 "
        pdb=" C13 IRX A 701 "
      ideal   model   delta    sigma   weight residual
     114.59   99.86   14.73 3.00e+00 1.11e-01 2.41e+01
  angle pdb=" CA  PRO A 258 "
        pdb=" N   PRO A 258 "
        pdb=" CD  PRO A 258 "
      ideal   model   delta    sigma   weight residual
     112.00  105.48    6.52 1.40e+00 5.10e-01 2.17e+01
  angle pdb=" C16 IRX A 701 "
        pdb=" C15 IRX A 701 "
        pdb=" N5  IRX A 701 "
      ideal   model   delta    sigma   weight residual
     115.43  128.43  -13.00 3.00e+00 1.11e-01 1.88e+01
  angle pdb=" C7  IRX A 701 "
        pdb=" C9  IRX A 701 "
        pdb=" N4  IRX A 701 "
      ideal   model   delta    sigma   weight residual
     113.70  101.29   12.41 3.00e+00 1.11e-01 1.71e+01
  ... (remaining 6631 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 2374
       16.91 -    33.82: 358
       33.82 -    50.73: 104
       50.73 -    67.63: 17
       67.63 -    84.54: 4
  Dihedral angle restraints: 2857
    sinusoidal: 1130
      harmonic: 1727
  Sorted by residual:
  dihedral pdb=" CA  HIS A 587 "
           pdb=" C   HIS A 587 "
           pdb=" N   MET A 588 "
           pdb=" CA  MET A 588 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.98   17.02     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  PHE A 484 "
           pdb=" C   PHE A 484 "
           pdb=" N   GLU A 485 "
           pdb=" CA  GLU A 485 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.52   16.48     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  HIS A 334 "
           pdb=" C   HIS A 334 "
           pdb=" N   PRO A 335 "
           pdb=" CA  PRO A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.18  -15.82     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 2854 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 433
       0.029 -    0.058: 220
       0.058 -    0.087: 54
       0.087 -    0.116: 40
       0.116 -    0.145: 10
  Chirality restraints: 757
  Sorted by residual:
  chirality pdb=" CA  VAL A 589 "
            pdb=" N   VAL A 589 "
            pdb=" C   VAL A 589 "
            pdb=" CB  VAL A 589 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CA  PHE A 257 "
            pdb=" N   PHE A 257 "
            pdb=" C   PHE A 257 "
            pdb=" CB  PHE A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.03e-01
  chirality pdb=" CA  ILE A 417 "
            pdb=" N   ILE A 417 "
            pdb=" C   ILE A 417 "
            pdb=" CB  ILE A 417 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.91e-01
  ... (remaining 754 not shown)

  Planarity restraints: 825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 257 "    0.080 5.00e-02 4.00e+02   1.19e-01 2.25e+01
        pdb=" N   PRO A 258 "   -0.205 5.00e-02 4.00e+02
        pdb=" CA  PRO A 258 "    0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO A 258 "    0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 649 "   -0.041 5.00e-02 4.00e+02   6.16e-02 6.08e+00
        pdb=" N   PRO A 650 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 650 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 650 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 292 "    0.031 5.00e-02 4.00e+02   4.66e-02 3.47e+00
        pdb=" N   PRO A 293 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 293 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 293 "    0.026 5.00e-02 4.00e+02
  ... (remaining 822 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1135
        2.79 -     3.32: 4565
        3.32 -     3.84: 7753
        3.84 -     4.37: 8514
        4.37 -     4.90: 14550
  Nonbonded interactions: 36517
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  98 "
            pdb=" OE1 GLU A 196 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   SER A 239 "
            pdb=" OG  SER A 239 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" N   GLN A 115 "
            pdb=" OE1 GLN A 115 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" OD1 ASN A  54 "
            pdb=" OG  SER A 160 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" OD2 ASP A 391 "
            pdb=" NZ  LYS A 396 "
     model   vdw
     2.349 3.120
  ... (remaining 36512 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 group one per residue
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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.360
  Find NCS groups from input model:        0.020
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6070
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      :  0.006   0.151   4897  Z= 0.286
  Angle     :  0.828  16.833   6636  Z= 0.386
  Chirality :  0.043   0.145    757
  Planarity :  0.006   0.119    825
  Dihedral  : 17.500  84.544   1745
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 27.41 %
    Favored  : 72.02 %
  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:  1.21 (0.37), residues: 590
  helix:  1.12 (0.35), residues: 250
  sheet:  1.69 (0.46), residues: 119
  loop :  0.04 (0.47), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 492 
 TYR   0.010   0.001   TYR A 462 
 PHE   0.020   0.002   PHE A 484 
 TRP   0.028   0.002   TRP A 427 
 HIS   0.009   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 ( 4897)
  covalent geometry    : angle       0.82772 ( 6636)
  hydrogen bonds       : bond        0.12716 (  277)
  hydrogen bonds       : angle       5.26091 (  768)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.174 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  443 ARG cc_start: 0.6188 (ttt-90) cc_final: 0.5610 (ttp-170)
REVERT: A  462 TYR cc_start: 0.8126 (p90) cc_final: 0.7718 (p90)
  outliers start: 3
  outliers final: 3
  residues processed: 60
  average time/residue: 0.0803
  time to fit residues: 6.1846
Evaluate side-chains
  61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0670
   chunk 31 optimal weight:    0.0470
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.4816

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.233910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.179689 restraints weight = 5864.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.179829 restraints weight = 11049.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.182533 restraints weight = 8332.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.181439 restraints weight = 5446.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.182730 restraints weight = 4596.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6509
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4897  Z= 0.126
  Angle     :  0.622   6.103   6636  Z= 0.315
  Chirality :  0.043   0.145    757
  Planarity :  0.005   0.070    825
  Dihedral  :  4.642  27.690    639
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  5.10 %
    Favored  : 94.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.36), residues: 590
  helix:  1.11 (0.34), residues: 253
  sheet:  1.81 (0.45), residues: 122
  loop : -0.09 (0.47), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 492 
 TYR   0.019   0.001   TYR A 181 
 PHE   0.022   0.002   PHE A 139 
 TRP   0.013   0.001   TRP A 427 
 HIS   0.006   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 4897)
  covalent geometry    : angle       0.62191 ( 6636)
  hydrogen bonds       : bond        0.04575 (  277)
  hydrogen bonds       : angle       4.74632 (  768)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.172 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 GLU cc_start: 0.7176 (pp20) cc_final: 0.6699 (pp20)
REVERT: A  385 LEU cc_start: 0.8201 (mm) cc_final: 0.7682 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 82
  average time/residue: 0.0768
  time to fit residues: 8.0802
Evaluate side-chains
  61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.227545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.171382 restraints weight = 5942.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.171800 restraints weight = 11170.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.172885 restraints weight = 8158.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.172661 restraints weight = 5479.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.173498 restraints weight = 4673.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6607
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4897  Z= 0.136
  Angle     :  0.625  10.151   6636  Z= 0.315
  Chirality :  0.044   0.147    757
  Planarity :  0.004   0.056    825
  Dihedral  :  4.601  26.931    639
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.78 %
    Favored  : 96.03 %
  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:  1.29 (0.36), residues: 590
  helix:  1.08 (0.34), residues: 245
  sheet:  2.08 (0.46), residues: 120
  loop :  0.01 (0.45), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 492 
 TYR   0.012   0.001   TYR A 181 
 PHE   0.017   0.001   PHE A 535 
 TRP   0.016   0.001   TRP A 427 
 HIS   0.003   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4897)
  covalent geometry    : angle       0.62534 ( 6636)
  hydrogen bonds       : bond        0.04899 (  277)
  hydrogen bonds       : angle       4.75900 (  768)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.188 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 GLU cc_start: 0.7318 (pp20) cc_final: 0.6849 (pp20)
REVERT: A  443 ARG cc_start: 0.6244 (ttm170) cc_final: 0.5984 (ttp-170)
  outliers start: 1
  outliers final: 1
  residues processed: 74
  average time/residue: 0.0726
  time to fit residues: 6.9370
Evaluate side-chains
  60 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0050
   chunk 21 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 53 optimal weight:   30.0000
   chunk 12 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 42 optimal weight:   20.0000
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.230552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.175215 restraints weight = 5890.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.173697 restraints weight = 11117.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.176376 restraints weight = 8573.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.175336 restraints weight = 5441.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.176620 restraints weight = 4886.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6547
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4897  Z= 0.116
  Angle     :  0.602  10.405   6636  Z= 0.299
  Chirality :  0.043   0.177    757
  Planarity :  0.004   0.055    825
  Dihedral  :  4.239  17.869    639
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.84 %
    Favored  : 96.98 %
  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:  1.39 (0.36), residues: 590
  helix:  1.25 (0.34), residues: 250
  sheet:  1.89 (0.46), residues: 122
  loop :  0.05 (0.47), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 466 
 TYR   0.018   0.001   TYR A 436 
 PHE   0.011   0.001   PHE A 288 
 TRP   0.013   0.002   TRP A 427 
 HIS   0.004   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4897)
  covalent geometry    : angle       0.60240 ( 6636)
  hydrogen bonds       : bond        0.04237 (  277)
  hydrogen bonds       : angle       4.48172 (  768)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.167 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 LEU cc_start: 0.8284 (mm) cc_final: 0.7723 (tt)
REVERT: A  436 TYR cc_start: 0.4448 (m-80) cc_final: 0.4072 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 76
  average time/residue: 0.0722
  time to fit residues: 7.0807
Evaluate side-chains
  60 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 38 optimal weight:   30.0000
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0370
   chunk 25 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A 342 GLN
** A 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.229324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.172058 restraints weight = 5772.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.173209 restraints weight = 10735.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.175683 restraints weight = 6945.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.174478 restraints weight = 4936.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.175806 restraints weight = 4247.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4897  Z= 0.110
  Angle     :  0.582   8.702   6636  Z= 0.289
  Chirality :  0.042   0.133    757
  Planarity :  0.004   0.055    825
  Dihedral  :  4.061  19.190    639
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  2.46 %
    Favored  : 97.16 %
  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:  1.51 (0.37), residues: 590
  helix:  1.27 (0.34), residues: 252
  sheet:  2.04 (0.46), residues: 121
  loop :  0.16 (0.48), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 466 
 TYR   0.007   0.001   TYR A 444 
 PHE   0.011   0.001   PHE A 257 
 TRP   0.013   0.001   TRP A 427 
 HIS   0.003   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 4897)
  covalent geometry    : angle       0.58199 ( 6636)
  hydrogen bonds       : bond        0.04059 (  277)
  hydrogen bonds       : angle       4.37957 (  768)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.165 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6323 (tm-30)
REVERT: A  385 LEU cc_start: 0.8271 (mm) cc_final: 0.7694 (tt)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.0663
  time to fit residues: 6.3646
Evaluate side-chains
  62 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 47 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   chunk 56 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0040
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.8396

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

Flipped N/Q/H residues before XYZ refinement:
A 439 GLN
** A 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.227853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.166020 restraints weight = 5951.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.154158 restraints weight = 5869.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.156230 restraints weight = 5643.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.157793 restraints weight = 3519.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.158406 restraints weight = 3059.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4897  Z= 0.125
  Angle     :  0.602   8.316   6636  Z= 0.302
  Chirality :  0.043   0.187    757
  Planarity :  0.004   0.055    825
  Dihedral  :  4.111  17.991    639
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.08 %
    Favored  : 97.73 %
  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:  1.53 (0.36), residues: 590
  helix:  1.33 (0.34), residues: 246
  sheet:  1.93 (0.44), residues: 122
  loop :  0.22 (0.48), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 492 
 TYR   0.010   0.001   TYR A 515 
 PHE   0.017   0.001   PHE A 139 
 TRP   0.012   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4897)
  covalent geometry    : angle       0.60164 ( 6636)
  hydrogen bonds       : bond        0.04485 (  277)
  hydrogen bonds       : angle       4.55089 (  768)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.176 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 ILE cc_start: 0.7872 (mm) cc_final: 0.7651 (mm)
REVERT: A  385 LEU cc_start: 0.8714 (mm) cc_final: 0.8035 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 75
  average time/residue: 0.0774
  time to fit residues: 7.4638
Evaluate side-chains
  60 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 47 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0870
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    1.3762

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

Flipped N/Q/H residues before XYZ refinement:
A 439 GLN
** A 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.221045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.162543 restraints weight = 5793.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.162108 restraints weight = 11685.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.165369 restraints weight = 8302.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.163759 restraints weight = 5337.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.165315 restraints weight = 4532.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4897  Z= 0.168
  Angle     :  0.666   8.678   6636  Z= 0.340
  Chirality :  0.045   0.145    757
  Planarity :  0.004   0.055    825
  Dihedral  :  4.281  18.568    639
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.65 %
    Favored  : 97.16 %
  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 (0.36), residues: 590
  helix:  1.09 (0.33), residues: 246
  sheet:  1.92 (0.44), residues: 122
  loop :  0.07 (0.47), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 492 
 TYR   0.007   0.001   TYR A 476 
 PHE   0.035   0.002   PHE A 378 
 TRP   0.013   0.002   TRP A 427 
 HIS   0.002   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4897)
  covalent geometry    : angle       0.66556 ( 6636)
  hydrogen bonds       : bond        0.05447 (  277)
  hydrogen bonds       : angle       4.70317 (  768)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.176 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 75
  average time/residue: 0.0789
  time to fit residues: 7.5396
Evaluate side-chains
  57 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 49 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 23 optimal weight:    0.3980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 439 GLN
** A 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.249428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.203368 restraints weight = 5940.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.199638 restraints weight = 13800.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.195387 restraints weight = 8937.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.196337 restraints weight = 6251.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.195181 restraints weight = 5372.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.4217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4897  Z= 0.170
  Angle     :  0.686   8.559   6636  Z= 0.350
  Chirality :  0.045   0.140    757
  Planarity :  0.004   0.055    825
  Dihedral  :  4.273  18.259    639
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.51 %
    Favored  : 98.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.35), residues: 590
  helix:  0.91 (0.33), residues: 246
  sheet:  1.97 (0.44), residues: 120
  loop : -0.07 (0.46), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 492 
 TYR   0.008   0.001   TYR A 476 
 PHE   0.028   0.002   PHE A 139 
 TRP   0.013   0.002   TRP A 637 
 HIS   0.002   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4897)
  covalent geometry    : angle       0.68649 ( 6636)
  hydrogen bonds       : bond        0.05559 (  277)
  hydrogen bonds       : angle       4.71061 (  768)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 ILE cc_start: 0.7724 (mm) cc_final: 0.7520 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 75
  average time/residue: 0.0723
  time to fit residues: 7.0895
Evaluate side-chains
  57 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0570
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 439 GLN
** A 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4777 r_free = 0.4777 target = 0.254834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.207912 restraints weight = 5845.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.204468 restraints weight = 11684.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.206142 restraints weight = 10696.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.203281 restraints weight = 7194.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.204792 restraints weight = 6817.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.4334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4897  Z= 0.126
  Angle     :  0.640   7.421   6636  Z= 0.319
  Chirality :  0.043   0.146    757
  Planarity :  0.004   0.055    825
  Dihedral  :  4.129  17.454    639
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.57 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.36), residues: 590
  helix:  1.00 (0.33), residues: 252
  sheet:  1.84 (0.44), residues: 122
  loop :  0.06 (0.47), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 492 
 TYR   0.008   0.001   TYR A 476 
 PHE   0.025   0.002   PHE A 378 
 TRP   0.013   0.001   TRP A 427 
 HIS   0.003   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4897)
  covalent geometry    : angle       0.63953 ( 6636)
  hydrogen bonds       : bond        0.04624 (  277)
  hydrogen bonds       : angle       4.49695 (  768)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.144 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 72
  average time/residue: 0.0710
  time to fit residues: 6.6387
Evaluate side-chains
  58 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 2 optimal weight:    0.7980
   chunk 47 optimal weight:   30.0000
   chunk 44 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 45 optimal weight:    9.9990
   chunk 1 optimal weight:    0.6980
   chunk 53 optimal weight:   40.0000
   chunk 58 optimal weight:    0.6980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 439 GLN
A 540 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.250469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.206894 restraints weight = 5858.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.203471 restraints weight = 13711.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.201855 restraints weight = 8835.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.200054 restraints weight = 7315.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.200785 restraints weight = 6195.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4897  Z= 0.157
  Angle     :  0.673   8.086   6636  Z= 0.341
  Chirality :  0.045   0.144    757
  Planarity :  0.004   0.055    825
  Dihedral  :  4.221  17.280    639
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.00 %
    Favored  : 99.81 %
  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:  1.08 (0.35), residues: 590
  helix:  0.92 (0.33), residues: 245
  sheet:  1.98 (0.45), residues: 120
  loop : -0.12 (0.45), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 492 
 TYR   0.007   0.001   TYR A 476 
 PHE   0.026   0.002   PHE A 139 
 TRP   0.013   0.002   TRP A 637 
 HIS   0.003   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4897)
  covalent geometry    : angle       0.67270 ( 6636)
  hydrogen bonds       : bond        0.05395 (  277)
  hydrogen bonds       : angle       4.63075 (  768)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.165 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 ILE cc_start: 0.7872 (mm) cc_final: 0.7539 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 72
  average time/residue: 0.0740
  time to fit residues: 6.9117
Evaluate side-chains
  59 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 28 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 41 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 52 optimal weight:   20.0000
   chunk 46 optimal weight:    0.0980
   chunk 40 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 439 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.251686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.207918 restraints weight = 5927.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.208352 restraints weight = 12963.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.210078 restraints weight = 9800.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.208608 restraints weight = 7220.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.209752 restraints weight = 5747.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.4373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4897  Z= 0.144
  Angle     :  0.663   7.570   6636  Z= 0.332
  Chirality :  0.044   0.145    757
  Planarity :  0.004   0.055    825
  Dihedral  :  4.185  16.771    639
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.00 %
    Favored  : 99.81 %
  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:  1.11 (0.36), residues: 590
  helix:  0.90 (0.33), residues: 251
  sheet:  2.02 (0.45), residues: 120
  loop : -0.09 (0.46), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 492 
 TYR   0.007   0.001   TYR A 476 
 PHE   0.020   0.002   PHE A 139 
 TRP   0.015   0.002   TRP A 637 
 HIS   0.003   0.001   HIS A 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4897)
  covalent geometry    : angle       0.66280 ( 6636)
  hydrogen bonds       : bond        0.05095 (  277)
  hydrogen bonds       : angle       4.56800 (  768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 877.02 seconds
wall clock time: 15 minutes 49.38 seconds (949.38 seconds total)