Starting phenix.real_space_refine
on Thu Mar  6 04:05:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ydq_33756/03_2025/7ydq_33756.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ydq_33756/03_2025/7ydq_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ydq_33756/03_2025/7ydq_33756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ydq_33756/03_2025/7ydq_33756.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ydq_33756/03_2025/7ydq_33756.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ydq_33756/03_2025/7ydq_33756.cif"
  }
  resolution = 4.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.23, per 1000 atoms: 0.68
  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: 1.16
  Conformation dependent library (CDL) restraints added in 551.2 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: 0.48
  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: 1.24

  Time building geometry restraints manager: 1.34 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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.670
  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:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.040
-------------------------------------------------------------------------------
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= 0.348
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.028   0.002   TRP A 427 
 HIS   0.009   0.001   HIS A 587 
 PHE   0.020   0.002   PHE A 484 
 TYR   0.010   0.001   TYR A 462 
 ARG   0.003   0.001   ARG A 492 

*********************** 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  : 0.473 
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: 0.1856
  time to fit residues: 14.2550
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  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 44 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 15 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0770
   chunk 46 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 34 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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 = 0.4512 r_free = 0.4512 target = 0.232897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.177324 restraints weight = 5809.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.177284 restraints weight = 11706.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.179917 restraints weight = 8855.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6498
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4897  Z= 0.165
  Angle     :  0.628   6.225   6636  Z= 0.319
  Chirality :  0.043   0.145    757
  Planarity :  0.005   0.072    825
  Dihedral  :  4.686  28.794    639
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.36), residues: 590
  helix:  1.08 (0.34), residues: 253
  sheet:  1.81 (0.46), residues: 122
  loop : -0.10 (0.47), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 587 
 PHE   0.022   0.002   PHE A 139 
 TYR   0.019   0.001   TYR A 181 
 ARG   0.002   0.000   ARG A 538 

*********************** 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
  79 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.477 
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: 0.7227 (pp20) cc_final: 0.6742 (pp20)
REVERT: A  340 ILE cc_start: 0.7671 (mm) cc_final: 0.7342 (mm)
REVERT: A  385 LEU cc_start: 0.8213 (mm) cc_final: 0.7678 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 79
  average time/residue: 0.1758
  time to fit residues: 17.7079
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  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 40 optimal weight:    0.0070
   chunk 50 optimal weight:   40.0000
   chunk 0 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 38 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9980
   overall best weight:    1.1802

-------------------------------------------------------------------------------
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 = 0.4449 r_free = 0.4449 target = 0.224982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.168090 restraints weight = 5841.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.166537 restraints weight = 12095.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.168550 restraints weight = 8501.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6672
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4897  Z= 0.206
  Angle     :  0.644  10.161   6636  Z= 0.326
  Chirality :  0.045   0.167    757
  Planarity :  0.005   0.059    825
  Dihedral  :  4.499  22.424    639
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.16 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.36), residues: 590
  helix:  0.96 (0.34), residues: 245
  sheet:  2.13 (0.46), residues: 120
  loop : -0.00 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 427 
 HIS   0.003   0.001   HIS A 551 
 PHE   0.018   0.002   PHE A 322 
 TYR   0.013   0.001   TYR A 444 
 ARG   0.003   0.000   ARG A 538 

*********************** 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
  75 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.546 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  436 TYR cc_start: 0.4994 (m-80) cc_final: 0.4726 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 75
  average time/residue: 0.1847
  time to fit residues: 17.7854
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  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 23 optimal weight:    0.0050
   chunk 56 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 35 optimal weight:   20.0000
   chunk 40 optimal weight:   10.0000
   overall best weight:    1.5400

-------------------------------------------------------------------------------
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 = 0.4418 r_free = 0.4418 target = 0.221679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.165667 restraints weight = 5959.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.167338 restraints weight = 11261.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.167413 restraints weight = 7251.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6701
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4897  Z= 0.249
  Angle     :  0.681  10.773   6636  Z= 0.347
  Chirality :  0.045   0.163    757
  Planarity :  0.005   0.056    825
  Dihedral  :  4.539  18.431    639
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.36), residues: 590
  helix:  0.76 (0.33), residues: 252
  sheet:  2.03 (0.46), residues: 120
  loop : -0.05 (0.47), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 637 
 HIS   0.005   0.001   HIS A 551 
 PHE   0.016   0.002   PHE A 139 
 TYR   0.009   0.001   TYR A 444 
 ARG   0.003   0.001   ARG A 443 

*********************** 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
  74 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.512 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  443 ARG cc_start: 0.6571 (ttp-170) cc_final: 0.6307 (tpp80)
  outliers start: 1
  outliers final: 1
  residues processed: 74
  average time/residue: 0.1707
  time to fit residues: 16.2997
Evaluate side-chains
  55 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 45 optimal weight:    9.9990
   chunk 28 optimal weight:    0.1980
   chunk 37 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 53 optimal weight:   30.0000
   chunk 56 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0670
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.4466 r_free = 0.4466 target = 0.227431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 142)---------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.167384 restraints weight = 5841.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.153435 restraints weight = 5052.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.157802 restraints weight = 5013.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4897  Z= 0.157
  Angle     :  0.609   8.757   6636  Z= 0.306
  Chirality :  0.043   0.154    757
  Planarity :  0.004   0.055    825
  Dihedral  :  4.342  16.628    639
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.16 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.36), residues: 590
  helix:  1.14 (0.34), residues: 245
  sheet:  2.00 (0.45), residues: 120
  loop :  0.14 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 551 
 PHE   0.033   0.001   PHE A 378 
 TYR   0.008   0.001   TYR A 444 
 ARG   0.003   0.001   ARG A 492 

*********************** 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
  76 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.518 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
REVERT: A  385 LEU cc_start: 0.8769 (mm) cc_final: 0.8219 (tt)
REVERT: A  443 ARG cc_start: 0.6316 (ttp-170) cc_final: 0.6065 (tpp80)
REVERT: A  588 MET cc_start: 0.4581 (mtt) cc_final: 0.3928 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 76
  average time/residue: 0.1737
  time to fit residues: 17.0685
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  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 47 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0770
   chunk 29 optimal weight:    0.0050
   overall best weight:    0.4752

-------------------------------------------------------------------------------
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 540 ASN
** 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 = 0.4469 r_free = 0.4469 target = 0.227323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.169053 restraints weight = 5749.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.166605 restraints weight = 10653.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.169653 restraints weight = 8059.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4897  Z= 0.152
  Angle     :  0.615   7.891   6636  Z= 0.307
  Chirality :  0.043   0.151    757
  Planarity :  0.004   0.056    825
  Dihedral  :  4.204  16.774    639
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.36), residues: 590
  helix:  1.25 (0.34), residues: 245
  sheet:  1.89 (0.44), residues: 120
  loop :  0.11 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 427 
 HIS   0.003   0.001   HIS A 551 
 PHE   0.024   0.001   PHE A 378 
 TYR   0.008   0.001   TYR A 476 
 ARG   0.003   0.001   ARG A 492 

*********************** 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
  77 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.480 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 PHE cc_start: 0.7885 (m-10) cc_final: 0.7682 (m-80)
REVERT: A  385 LEU cc_start: 0.8179 (mm) cc_final: 0.7619 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 77
  average time/residue: 0.1685
  time to fit residues: 16.7811
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  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 56 optimal weight:    0.3980
   chunk 40 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4440 r_free = 0.4440 target = 0.224626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.166214 restraints weight = 5691.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.165758 restraints weight = 10269.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.168219 restraints weight = 7326.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4897  Z= 0.163
  Angle     :  0.623   8.483   6636  Z= 0.311
  Chirality :  0.043   0.154    757
  Planarity :  0.004   0.055    825
  Dihedral  :  4.134  15.673    639
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.36), residues: 590
  helix:  1.21 (0.34), residues: 245
  sheet:  2.20 (0.45), residues: 118
  loop :  0.04 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 427 
 HIS   0.005   0.001   HIS A 551 
 PHE   0.020   0.001   PHE A  36 
 TYR   0.008   0.001   TYR A 515 
 ARG   0.004   0.001   ARG A 492 

*********************** 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
  74 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.538 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  385 LEU cc_start: 0.8273 (mm) cc_final: 0.7737 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 74
  average time/residue: 0.1884
  time to fit residues: 18.1115
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  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 32 optimal weight:    0.0030
   chunk 33 optimal weight:    0.9990
   chunk 54 optimal weight:   40.0000
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 1 optimal weight:    0.7980
   chunk 3 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.0594

-------------------------------------------------------------------------------
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
A 554 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.223365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.163329 restraints weight = 5902.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.165506 restraints weight = 11094.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.167927 restraints weight = 6876.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6683
moved from start:          0.3004

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= 0.200
  Angle     :  0.685   9.257   6636  Z= 0.338
  Chirality :  0.045   0.193    757
  Planarity :  0.004   0.056    825
  Dihedral  :  4.242  15.510    639
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.35), residues: 590
  helix:  1.08 (0.33), residues: 246
  sheet:  1.93 (0.43), residues: 119
  loop :  0.03 (0.45), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 427 
 HIS   0.003   0.001   HIS A 108 
 PHE   0.019   0.002   PHE A 378 
 TYR   0.006   0.001   TYR A 570 
 ARG   0.006   0.001   ARG A 492 

*********************** 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
  70 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.518 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
REVERT: A  111 PHE cc_start: 0.7754 (m-80) cc_final: 0.7507 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 70
  average time/residue: 0.1752
  time to fit residues: 15.7654
Evaluate side-chains
  54 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 31 optimal weight:    0.0010
   chunk 11 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.7190

-------------------------------------------------------------------------------
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 = 0.4465 r_free = 0.4465 target = 0.226913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.184814 restraints weight = 5848.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.182275 restraints weight = 14012.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.183330 restraints weight = 11573.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6539
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4897  Z= 0.174
  Angle     :  0.657   8.692   6636  Z= 0.323
  Chirality :  0.044   0.152    757
  Planarity :  0.004   0.056    825
  Dihedral  :  4.186  15.452    639
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.38 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.35), residues: 590
  helix:  1.17 (0.34), residues: 245
  sheet:  1.93 (0.43), residues: 119
  loop :  0.02 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 427 
 HIS   0.004   0.001   HIS A 587 
 PHE   0.017   0.001   PHE A 378 
 TYR   0.012   0.001   TYR A 476 
 ARG   0.005   0.001   ARG A 492 

*********************** 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
  69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.526 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 69
  average time/residue: 0.1744
  time to fit residues: 15.7045
Evaluate side-chains
  55 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0980
   chunk 45 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0980
   chunk 39 optimal weight:    0.5980
   chunk 41 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4464 r_free = 0.4464 target = 0.226779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.170436 restraints weight = 5863.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.161440 restraints weight = 9594.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.165481 restraints weight = 9246.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
moved from start:          0.3167

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= 0.170
  Angle     :  0.653   8.601   6636  Z= 0.320
  Chirality :  0.043   0.153    757
  Planarity :  0.004   0.056    825
  Dihedral  :  4.198  16.419    639
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.76 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.35), residues: 590
  helix:  1.18 (0.34), residues: 245
  sheet:  1.99 (0.44), residues: 119
  loop :  0.01 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 427 
 HIS   0.005   0.001   HIS A 587 
 PHE   0.016   0.001   PHE A 378 
 TYR   0.013   0.001   TYR A 476 
 ARG   0.007   0.001   ARG A 443 

********************** 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
  69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.524 
Fit side-chains
TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  569 HIS cc_start: 0.5821 (p90) cc_final: 0.5608 (p90)
  outliers start: 1
  outliers final: 1
  residues processed: 69
  average time/residue: 0.1742
  time to fit residues: 15.6696
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  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0770
   chunk 55 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0980
   chunk 49 optimal weight:   30.0000
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.2344

-------------------------------------------------------------------------------
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 = 0.4415 r_free = 0.4415 target = 0.221062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.162859 restraints weight = 5848.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.162628 restraints weight = 11416.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.164566 restraints weight = 8459.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.3246

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= 0.218
  Angle     :  0.689   9.509   6636  Z= 0.343
  Chirality :  0.045   0.152    757
  Planarity :  0.004   0.056    825
  Dihedral  :  4.310  17.262    639
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.19 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.36), residues: 590
  helix:  0.97 (0.33), residues: 252
  sheet:  2.03 (0.44), residues: 119
  loop :  0.03 (0.46), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 427 
 HIS   0.005   0.001   HIS A 587 
 PHE   0.021   0.002   PHE A 378 
 TYR   0.011   0.001   TYR A 476 
 ARG   0.005   0.001   ARG A 492 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1708.64 seconds
wall clock time: 30 minutes 23.51 seconds (1823.51 seconds total)