Starting phenix.real_space_refine
on Fri Aug 22 21:37:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qbg_52998/08_2025/9qbg_52998.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qbg_52998/08_2025/9qbg_52998.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qbg_52998/08_2025/9qbg_52998.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qbg_52998/08_2025/9qbg_52998.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qbg_52998/08_2025/9qbg_52998.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qbg_52998/08_2025/9qbg_52998.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    2437      2.51       5
     N     702      2.21       5
     O     737      1.98       5
     H    3767      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7684
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 7684
          Classifications: {'peptide': 508}
          Link IDs: {'PTRANS': 29, 'TRANS': 478}
          Chain breaks: 2
  Time building chain proxies: 1.84, per 1000 atoms: 0.24
  Number of scatterers: 7684
  At special positions: 0
  Unit cell: (65.1, 89.838, 83.328, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     O     737      8.00
     N     702      7.00
     C    2437      6.00
     H    3767      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  53 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 192 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 204 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 199 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 227 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 224 " - pdb=" SG  CYS A 235 " distance=2.14
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 244 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 252 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 255 " - pdb=" SG  CYS A 264 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 268 " - pdb=" SG  CYS A 295 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 311 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 315 " - pdb=" SG  CYS A 331 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 334 " - pdb=" SG  CYS A 338 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 342 " - pdb=" SG  CYS A 367 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 475 " - pdb=" SG  CYS A 504 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 520 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 528 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 531 " - pdb=" SG  CYS A 540 " distance=2.02

  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: 0.70
  Conformation dependent library (CDL) restraints added in 357.4 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  934

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 9 sheets defined
      22.4% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 41 through 51
    Processing helix  chain 'A' and resid 71 through 77
      removed outlier: 4.258A  pdb=" N   ASP A  76 " --> pdb=" O   PHE A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 110
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 199 through 203
    Processing helix  chain 'A' and resid 208 through 212
      removed outlier: 4.053A  pdb=" N   CYS A 212 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 224
      removed outlier: 3.517A  pdb=" N   CYS A 224 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 235
    Processing helix  chain 'A' and resid 347 through 351
    Processing helix  chain 'A' and resid 360 through 365
    Processing helix  chain 'A' and resid 377 through 383
    Processing helix  chain 'A' and resid 384 through 388
    Processing helix  chain 'A' and resid 393 through 401
      removed outlier: 3.860A  pdb=" N   GLN A 398 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
    Processing helix  chain 'A' and resid 436 through 439
    Processing helix  chain 'A' and resid 481 through 485
      removed outlier: 3.542A  pdb=" N   GLN A 484 " --> pdb=" O   PRO A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 506
    Processing helix  chain 'A' and resid 515 through 519
    Processing helix  chain 'A' and resid 524 through 528
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.794A  pdb=" N   CYS A  26 " --> pdb=" O   GLN A  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63
      removed outlier: 6.587A  pdb=" N   LEU A  60 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   ALA A  87 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   LEU A  62 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   GLY A 152 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL A 153 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260
    Processing sheet with id=AA4, first strand: chain 'A' and resid 272 through 274
    Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 291
    Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 312
    Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 370
    Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 376
      removed outlier: 5.751A  pdb=" N   LEU A 465 " --> pdb=" O   TYR A 441 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ALA A 466 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 8.389A  pdb=" N   THR A 496 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ILE A 468 " --> pdb=" O   THR A 496 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   ASN A 498 " --> pdb=" O   ILE A 468 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   HIS A 470 " --> pdb=" O   ASN A 498 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 534 through 536

    93 hydrogen bonds defined for protein.
    159 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        0.95 -     1.14: 3767
        1.14 -     1.33: 1241
        1.33 -     1.53: 2245
        1.53 -     1.72: 473
        1.72 -     1.91: 45
  Bond restraints: 7771
  Sorted by residual:
  bond pdb=" NE1 TRP A 169 "
       pdb=" HE1 TRP A 169 "
    ideal  model  delta    sigma   weight residual
    0.860  1.052 -0.192 2.00e-02 2.50e+03 9.24e+01
  bond pdb=" NE  ARG A 434 "
       pdb=" HE  ARG A 434 "
    ideal  model  delta    sigma   weight residual
    0.860  1.046 -0.186 2.00e-02 2.50e+03 8.61e+01
  bond pdb=" NE2 HIS A 349 "
       pdb=" HE2 HIS A 349 "
    ideal  model  delta    sigma   weight residual
    0.860  1.045 -0.185 2.00e-02 2.50e+03 8.55e+01
  bond pdb=" NE1 TRP A 415 "
       pdb=" HE1 TRP A 415 "
    ideal  model  delta    sigma   weight residual
    0.860  1.045 -0.185 2.00e-02 2.50e+03 8.53e+01
  bond pdb=" NH2 ARG A 340 "
       pdb="HH22 ARG A 340 "
    ideal  model  delta    sigma   weight residual
    0.860  1.043 -0.183 2.00e-02 2.50e+03 8.42e+01
  ... (remaining 7766 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 11076
        2.19 -     4.38: 2024
        4.38 -     6.56: 670
        6.56 -     8.75: 223
        8.75 -    10.94: 33
  Bond angle restraints: 14026
  Sorted by residual:
  angle pdb=" C   GLY A 229 "
        pdb=" N   PRO A 230 "
        pdb=" CA  PRO A 230 "
      ideal   model   delta    sigma   weight residual
     119.87  127.85   -7.98 1.04e+00 9.25e-01 5.89e+01
  angle pdb=" C   ASN A 488 "
        pdb=" N   PRO A 489 "
        pdb=" CA  PRO A 489 "
      ideal   model   delta    sigma   weight residual
     119.82  127.30   -7.48 9.80e-01 1.04e+00 5.82e+01
  angle pdb=" C   ASP A 384 "
        pdb=" N   PRO A 385 "
        pdb=" CA  PRO A 385 "
      ideal   model   delta    sigma   weight residual
     119.56  127.31   -7.75 1.02e+00 9.61e-01 5.77e+01
  angle pdb=" C   GLY A 524 "
        pdb=" N   PRO A 525 "
        pdb=" CA  PRO A 525 "
      ideal   model   delta    sigma   weight residual
     119.56  127.23   -7.67 1.02e+00 9.61e-01 5.65e+01
  angle pdb=" C   LEU A 419 "
        pdb=" N   PRO A 420 "
        pdb=" CA  PRO A 420 "
      ideal   model   delta    sigma   weight residual
     119.87  127.39   -7.52 1.04e+00 9.25e-01 5.22e+01
  ... (remaining 14021 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 3515
       17.47 -    34.93: 146
       34.93 -    52.40: 43
       52.40 -    69.87: 22
       69.87 -    87.33: 8
  Dihedral angle restraints: 3734
    sinusoidal: 2056
      harmonic: 1678
  Sorted by residual:
  dihedral pdb=" N   VAL A  91 "
           pdb=" C   VAL A  91 "
           pdb=" CA  VAL A  91 "
           pdb=" CB  VAL A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  115.00    8.40     0      2.50e+00 1.60e-01 1.13e+01
  dihedral pdb=" C   LEU A 154 "
           pdb=" N   LEU A 154 "
           pdb=" CA  LEU A 154 "
           pdb=" CB  LEU A 154 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.68   -7.92     0      2.50e+00 1.60e-01 1.00e+01
  dihedral pdb=" CB  CYS A 531 "
           pdb=" SG  CYS A 531 "
           pdb=" SG  CYS A 540 "
           pdb=" CB  CYS A 540 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   67.61   25.39     1      1.00e+01 1.00e-02 9.27e+00
  ... (remaining 3731 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 296
       0.061 -    0.121: 188
       0.121 -    0.182: 91
       0.182 -    0.243: 26
       0.243 -    0.303: 6
  Chirality restraints: 607
  Sorted by residual:
  chirality pdb=" CG  LEU A 465 "
            pdb=" CB  LEU A 465 "
            pdb=" CD1 LEU A 465 "
            pdb=" CD2 LEU A 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CB  VAL A  91 "
            pdb=" CA  VAL A  91 "
            pdb=" CG1 VAL A  91 "
            pdb=" CG2 VAL A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CA  ASN A 111 "
            pdb=" N   ASN A 111 "
            pdb=" C   ASN A 111 "
            pdb=" CB  ASN A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 604 not shown)

  Planarity restraints: 1197
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 163 "   -0.062 2.00e-02 2.50e+03   2.51e-02 1.89e+01
        pdb=" CG  TYR A 163 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 163 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 163 "    0.020 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 163 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 163 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 163 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 163 "   -0.045 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 163 "    0.009 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 163 "    0.010 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 163 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 163 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 279 "   -0.057 2.00e-02 2.50e+03   2.37e-02 1.69e+01
        pdb=" CG  PHE A 279 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 279 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 279 "    0.023 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 279 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 279 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 279 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 279 "    0.002 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 279 "    0.003 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 279 "   -0.013 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 279 "   -0.013 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 279 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 258 "    0.056 2.00e-02 2.50e+03   2.16e-02 1.40e+01
        pdb=" CG  PHE A 258 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 258 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 258 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 258 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 258 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 258 "    0.002 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 258 "   -0.018 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 258 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 258 "    0.013 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 258 "    0.005 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 258 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1194 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 690
        2.17 -     2.78: 14702
        2.78 -     3.38: 22658
        3.38 -     3.99: 31057
        3.99 -     4.60: 45433
  Nonbonded interactions: 114540
  Sorted by model distance:
  nonbonded pdb=" H   LEU A 313 "
            pdb=" H   VAL A 314 "
     model   vdw
     1.560 2.100
  nonbonded pdb=" OE1 GLN A  57 "
            pdb=" HH  TYR A 303 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" OE1 GLN A 164 "
            pdb=" H   GLN A 164 "
     model   vdw
     1.638 2.450
  nonbonded pdb=" HH  TYR A 301 "
            pdb=" OE2 GLU A 460 "
     model   vdw
     1.647 2.450
  nonbonded pdb=" OE1 GLU A 325 "
            pdb=" H   GLU A 325 "
     model   vdw
     1.649 2.450
  ... (remaining 114535 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:             0.530
  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:             0.050
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.560
  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:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
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      :  0.021   0.135   4022  Z= 1.163
  Angle     :  1.861  10.939   5479  Z= 1.247
  Chirality :  0.096   0.303    607
  Planarity :  0.009   0.033    720
  Dihedral  : 11.301  87.333   1463
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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 aren not related in a simple way.
  whole:  0.66 (0.37), residues: 502
  helix: -3.13 (0.59), residues: 44
  sheet: -0.24 (0.67), residues: 53
  loop :  1.14 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  92 
 TYR   0.057   0.011   TYR A 163 
 PHE   0.040   0.007   PHE A 279 
 TRP   0.028   0.008   TRP A 482 
 HIS   0.011   0.002   HIS A 469 

Details of bonding type rmsd
  covalent geometry    : bond        0.02119 ( 4004)
  covalent geometry    : angle       1.85787 ( 5443)
  SS BOND              : bond        0.02863 (   18)
  SS BOND              : angle       2.26605 (   36)
  hydrogen bonds       : bond        0.19297 (   93)
  hydrogen bonds       : angle       8.87165 (  159)

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

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

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ILE cc_start: 0.9084 (mt) cc_final: 0.8868 (mt)
REVERT: A  347 MET cc_start: 0.8546 (mmm) cc_final: 0.8037 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2575
  time to fit residues: 14.5218
Evaluate side-chains
  25 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 257 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.066072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.055561 restraints weight = 54112.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.058214 restraints weight = 23361.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.059937 restraints weight = 12700.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.061139 restraints weight = 8077.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.061879 restraints weight = 5711.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4022  Z= 0.161
  Angle     :  0.697   7.151   5479  Z= 0.383
  Chirality :  0.047   0.162    607
  Planarity :  0.005   0.048    720
  Dihedral  :  5.829  24.288    545
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  3.67 %
    Favored  : 95.64 %
  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 aren not related in a simple way.
  whole:  0.20 (0.37), residues: 502
  helix: -1.63 (0.78), residues: 36
  sheet: -0.83 (0.64), residues: 58
  loop :  0.57 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 103 
 TYR   0.017   0.002   TYR A 163 
 PHE   0.012   0.002   PHE A 258 
 TRP   0.007   0.001   TRP A 482 
 HIS   0.010   0.002   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4004)
  covalent geometry    : angle       0.68946 ( 5443)
  SS BOND              : bond        0.00529 (   18)
  SS BOND              : angle       1.41810 (   36)
  hydrogen bonds       : bond        0.05266 (   93)
  hydrogen bonds       : angle       7.53045 (  159)

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

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

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 MET cc_start: 0.8885 (mmm) cc_final: 0.8402 (mmm)
  outliers start: 3
  outliers final: 1
  residues processed: 35
  average time/residue: 0.1184
  time to fit residues: 5.1428
Evaluate side-chains
  27 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.1980
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 ASN ** 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 = 0.3715 r_free = 0.3715 target = 0.064487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.053966 restraints weight = 55346.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.056553 restraints weight = 24210.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.058208 restraints weight = 13388.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.059337 restraints weight = 8664.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.060092 restraints weight = 6220.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   4022  Z= 0.180
  Angle     :  0.632   6.342   5479  Z= 0.341
  Chirality :  0.044   0.141    607
  Planarity :  0.004   0.028    720
  Dihedral  :  5.553  26.280    545
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  4.59 %
    Favored  : 94.95 %
  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 aren not related in a simple way.
  whole:  0.27 (0.38), residues: 502
  helix: -1.29 (0.81), residues: 37
  sheet: -0.15 (0.68), residues: 68
  loop :  0.50 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 432 
 TYR   0.018   0.002   TYR A 163 
 PHE   0.013   0.002   PHE A 381 
 TRP   0.007   0.001   TRP A 482 
 HIS   0.005   0.001   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 4004)
  covalent geometry    : angle       0.62137 ( 5443)
  SS BOND              : bond        0.00373 (   18)
  SS BOND              : angle       1.56341 (   36)
  hydrogen bonds       : bond        0.04438 (   93)
  hydrogen bonds       : angle       7.35239 (  159)

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

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

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 28
  average time/residue: 0.1116
  time to fit residues: 4.2212
Evaluate side-chains
  24 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  253 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0870
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   overall best weight:    0.9160

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

Flipped N/Q/H residues before XYZ refinement:
A  88 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.063568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.053074 restraints weight = 56580.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.055632 restraints weight = 24190.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.057193 restraints weight = 13214.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.058341 restraints weight = 8603.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.059069 restraints weight = 6159.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.3639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4022  Z= 0.123
  Angle     :  0.563   5.142   5479  Z= 0.299
  Chirality :  0.043   0.146    607
  Planarity :  0.003   0.024    720
  Dihedral  :  5.257  20.940    545
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  5.05 %
    Favored  : 94.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.39), residues: 502
  helix: -0.89 (0.87), residues: 37
  sheet: -0.22 (0.68), residues: 68
  loop :  0.56 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 517 
 TYR   0.015   0.002   TYR A 163 
 PHE   0.007   0.001   PHE A 381 
 TRP   0.006   0.001   TRP A 482 
 HIS   0.004   0.001   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4004)
  covalent geometry    : angle       0.55956 ( 5443)
  SS BOND              : bond        0.00320 (   18)
  SS BOND              : angle       0.98028 (   36)
  hydrogen bonds       : bond        0.03631 (   93)
  hydrogen bonds       : angle       6.81039 (  159)

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

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

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 MET cc_start: 0.9162 (mmm) cc_final: 0.8667 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 22
  average time/residue: 0.0884
  time to fit residues: 2.7624
Evaluate side-chains
  22 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  42 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.063690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.053176 restraints weight = 55659.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.055688 restraints weight = 24037.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.057244 restraints weight = 13241.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.058396 restraints weight = 8626.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.059158 restraints weight = 6199.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4022  Z= 0.111
  Angle     :  0.532   4.576   5479  Z= 0.280
  Chirality :  0.042   0.141    607
  Planarity :  0.003   0.026    720
  Dihedral  :  4.916  18.045    545
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  5.28 %
    Favored  : 94.27 %
  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 aren not related in a simple way.
  whole:  0.43 (0.40), residues: 502
  helix: -0.72 (0.90), residues: 37
  sheet: -0.17 (0.68), residues: 68
  loop :  0.59 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  47 
 TYR   0.014   0.002   TYR A 163 
 PHE   0.005   0.001   PHE A 381 
 TRP   0.008   0.001   TRP A 415 
 HIS   0.004   0.001   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4004)
  covalent geometry    : angle       0.52932 ( 5443)
  SS BOND              : bond        0.00307 (   18)
  SS BOND              : angle       0.81135 (   36)
  hydrogen bonds       : bond        0.03292 (   93)
  hydrogen bonds       : angle       6.47924 (  159)

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

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

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 MET cc_start: 0.9146 (mmm) cc_final: 0.8686 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 21
  average time/residue: 0.1090
  time to fit residues: 3.1449
Evaluate side-chains
  20 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  253 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 484 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.062850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.052479 restraints weight = 57427.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.054979 restraints weight = 24533.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.056558 restraints weight = 13338.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.057649 restraints weight = 8562.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.058341 restraints weight = 6133.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4022  Z= 0.166
  Angle     :  0.541   4.764   5479  Z= 0.288
  Chirality :  0.042   0.135    607
  Planarity :  0.003   0.026    720
  Dihedral  :  4.769  15.391    545
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  6.19 %
    Favored  : 93.58 %
  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 aren not related in a simple way.
  whole:  0.46 (0.40), residues: 502
  helix:  0.01 (0.97), residues: 31
  sheet: -0.20 (0.67), residues: 68
  loop :  0.53 (0.34), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 517 
 TYR   0.012   0.002   TYR A 163 
 PHE   0.007   0.001   PHE A 364 
 TRP   0.005   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4004)
  covalent geometry    : angle       0.53809 ( 5443)
  SS BOND              : bond        0.00342 (   18)
  SS BOND              : angle       0.90149 (   36)
  hydrogen bonds       : bond        0.03329 (   93)
  hydrogen bonds       : angle       6.21953 (  159)

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

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

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 MET cc_start: 0.9140 (mmm) cc_final: 0.8911 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 19
  average time/residue: 0.1127
  time to fit residues: 2.9629
Evaluate side-chains
  18 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 0 optimal weight:    0.6980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
** A 249 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 = 0.3664 r_free = 0.3664 target = 0.063293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.053053 restraints weight = 56932.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.055537 restraints weight = 24356.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.057098 restraints weight = 13358.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.058192 restraints weight = 8623.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.058879 restraints weight = 6198.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.4386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4022  Z= 0.114
  Angle     :  0.497   4.533   5479  Z= 0.262
  Chirality :  0.042   0.137    607
  Planarity :  0.003   0.025    720
  Dihedral  :  4.569  15.087    545
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  5.96 %
    Favored  : 93.58 %
  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 aren not related in a simple way.
  whole:  0.52 (0.40), residues: 502
  helix:  0.20 (1.01), residues: 31
  sheet: -0.19 (0.67), residues: 68
  loop :  0.56 (0.34), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 432 
 TYR   0.012   0.001   TYR A 163 
 PHE   0.005   0.001   PHE A 108 
 TRP   0.005   0.001   TRP A 169 
 HIS   0.002   0.001   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4004)
  covalent geometry    : angle       0.49529 ( 5443)
  SS BOND              : bond        0.00221 (   18)
  SS BOND              : angle       0.72079 (   36)
  hydrogen bonds       : bond        0.03149 (   93)
  hydrogen bonds       : angle       6.06615 (  159)

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

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

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 MET cc_start: 0.9136 (mmm) cc_final: 0.8912 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 18
  average time/residue: 0.1059
  time to fit residues: 2.6497
Evaluate side-chains
  19 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  253 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 0 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 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 = 0.3661 r_free = 0.3661 target = 0.063246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.052878 restraints weight = 56923.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.055379 restraints weight = 24754.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.056943 restraints weight = 13644.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.058045 restraints weight = 8822.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.058723 restraints weight = 6343.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.4556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4022  Z= 0.105
  Angle     :  0.493   4.804   5479  Z= 0.257
  Chirality :  0.042   0.136    607
  Planarity :  0.003   0.024    720
  Dihedral  :  4.446  14.541    545
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  6.19 %
    Favored  : 93.58 %
  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 aren not related in a simple way.
  whole:  0.56 (0.41), residues: 502
  helix:  0.33 (1.03), residues: 31
  sheet: -0.18 (0.67), residues: 68
  loop :  0.59 (0.34), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  47 
 TYR   0.010   0.001   TYR A 163 
 PHE   0.005   0.001   PHE A 534 
 TRP   0.005   0.001   TRP A 169 
 HIS   0.003   0.001   HIS A 469 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 4004)
  covalent geometry    : angle       0.49127 ( 5443)
  SS BOND              : bond        0.00194 (   18)
  SS BOND              : angle       0.69742 (   36)
  hydrogen bonds       : bond        0.03060 (   93)
  hydrogen bonds       : angle       5.97582 (  159)

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

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

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 MET cc_start: 0.9100 (mmm) cc_final: 0.8886 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 20
  average time/residue: 0.1483
  time to fit residues: 3.7440
Evaluate side-chains
  19 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.062764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.052165 restraints weight = 58205.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.054694 restraints weight = 25385.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.056270 restraints weight = 14093.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.057349 restraints weight = 9188.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.058052 restraints weight = 6715.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.4752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4022  Z= 0.113
  Angle     :  0.486   4.562   5479  Z= 0.255
  Chirality :  0.042   0.135    607
  Planarity :  0.003   0.026    720
  Dihedral  :  4.358  14.131    545
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  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 aren not related in a simple way.
  whole:  0.55 (0.41), residues: 502
  helix:  0.37 (1.05), residues: 31
  sheet: -0.24 (0.67), residues: 68
  loop :  0.59 (0.35), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 517 
 TYR   0.011   0.002   TYR A 163 
 PHE   0.006   0.001   PHE A 534 
 TRP   0.004   0.001   TRP A 169 
 HIS   0.002   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 4004)
  covalent geometry    : angle       0.48423 ( 5443)
  SS BOND              : bond        0.00208 (   18)
  SS BOND              : angle       0.73340 (   36)
  hydrogen bonds       : bond        0.02996 (   93)
  hydrogen bonds       : angle       5.89488 (  159)

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

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

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LYS cc_start: 0.9021 (pttp) cc_final: 0.8763 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.1140
  time to fit residues: 2.9998
Evaluate side-chains
  18 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   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  68 ASN
** A 237 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 = 0.3671 r_free = 0.3671 target = 0.063701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.053203 restraints weight = 56449.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.055707 restraints weight = 24449.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.057302 restraints weight = 13561.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.058412 restraints weight = 8823.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.059110 restraints weight = 6394.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.4875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4022  Z= 0.090
  Angle     :  0.478   4.406   5479  Z= 0.247
  Chirality :  0.042   0.135    607
  Planarity :  0.003   0.025    720
  Dihedral  :  4.271  13.897    545
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  6.19 %
    Favored  : 93.35 %
  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 aren not related in a simple way.
  whole:  0.63 (0.41), residues: 502
  helix:  0.43 (1.05), residues: 31
  sheet: -0.15 (0.67), residues: 68
  loop :  0.64 (0.35), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  47 
 TYR   0.008   0.001   TYR A 163 
 PHE   0.005   0.001   PHE A 534 
 TRP   0.005   0.001   TRP A 169 
 HIS   0.002   0.001   HIS A 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 4004)
  covalent geometry    : angle       0.47670 ( 5443)
  SS BOND              : bond        0.00173 (   18)
  SS BOND              : angle       0.66601 (   36)
  hydrogen bonds       : bond        0.02924 (   93)
  hydrogen bonds       : angle       5.79101 (  159)

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

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

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1004 Ramachandran restraints generated.
    502 Oldfield, 0 Emsley, 502 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8842 (pt)
REVERT: A  347 MET cc_start: 0.8818 (mmm) cc_final: 0.8421 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0990
  time to fit residues: 2.9247
Evaluate side-chains
  20 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 46 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 27 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 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 = 0.3659 r_free = 0.3659 target = 0.063053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.052581 restraints weight = 57635.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.055067 restraints weight = 25381.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.056654 restraints weight = 14140.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.057752 restraints weight = 9264.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.058435 restraints weight = 6727.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.4989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4022  Z= 0.116
  Angle     :  0.486   4.476   5479  Z= 0.253
  Chirality :  0.042   0.133    607
  Planarity :  0.003   0.027    720
  Dihedral  :  4.265  13.996    545
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  6.19 %
    Favored  : 93.35 %
  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 aren not related in a simple way.
  whole:  0.64 (0.41), residues: 502
  helix:  0.25 (1.02), residues: 31
  sheet:  0.10 (0.74), residues: 58
  loop :  0.60 (0.34), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 103 
 TYR   0.009   0.001   TYR A 112 
 PHE   0.006   0.001   PHE A 534 
 TRP   0.005   0.001   TRP A 521 
 HIS   0.002   0.001   HIS A 469 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4004)
  covalent geometry    : angle       0.48391 ( 5443)
  SS BOND              : bond        0.00196 (   18)
  SS BOND              : angle       0.73050 (   36)
  hydrogen bonds       : bond        0.02925 (   93)
  hydrogen bonds       : angle       5.81620 (  159)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1501.80 seconds
wall clock time: 26 minutes 7.48 seconds (1567.48 seconds total)