Starting phenix.real_space_refine
on Tue Mar  3 11:04:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8di5_27439/03_2026/8di5_27439.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8di5_27439/03_2026/8di5_27439.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8di5_27439/03_2026/8di5_27439.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8di5_27439/03_2026/8di5_27439.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8di5_27439/03_2026/8di5_27439.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8di5_27439/03_2026/8di5_27439.cif"
  }
  resolution = 3.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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      12      5.16       5
     C    1573      2.51       5
     N     409      2.21       5
     O     473      1.98       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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2467
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1546
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "H"
      Number of atoms: 907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 907
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 3, 'TRANS': 112}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.61, per 1000 atoms: 0.25
  Number of scatterers: 2467
  At special positions: 0
  Unit cell: (68, 79, 73, 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      12     16.00
     O     473      8.00
     N     409      7.00
     C    1573      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG C1301 " - " ASN C 343 "
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 91.8 milliseconds
  

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  568

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 5 sheets defined
      15.8% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 365 through 371
    Processing helix  chain 'C' and resid 383 through 387
      removed outlier: 3.645A  pdb=" N   LEU C 387 " --> pdb=" O   PRO C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 5.008A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 438 through 443
    Processing helix  chain 'H' and resid 53 through 55
      No H-bonds generated for 'chain 'H' and resid 53 through 55'
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 3.962A  pdb=" N   LYS H  64 " --> pdb=" O   PRO H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 4.065A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 5.268A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 7
    Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.296A  pdb=" N   GLU H  33 " --> pdb=" O   VAL H  98 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   MET H  34 " --> pdb=" O   ASN H  50 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   ASN H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12

    80 hydrogen bonds defined for protein.
    204 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.23

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 786
        1.34 -     1.46: 698
        1.46 -     1.58: 1036
        1.58 -     1.70: 0
        1.70 -     1.82: 14
  Bond restraints: 2534
  Sorted by residual:
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.50e+00
  bond pdb=" CB  TRP H  47 "
       pdb=" CG  TRP H  47 "
    ideal  model  delta    sigma   weight residual
    1.498  1.450  0.048 3.10e-02 1.04e+03 2.39e+00
  bond pdb=" CB  ILE C 472 "
       pdb=" CG2 ILE C 472 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.22e+00
  bond pdb=" CB  ASN H  83 "
       pdb=" CG  ASN H  83 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 2.50e-02 1.60e+03 1.75e+00
  bond pdb=" CG  LEU C 452 "
       pdb=" CD1 LEU C 452 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.67e+00
  ... (remaining 2529 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.77: 3417
        3.77 -     7.54: 26
        7.54 -    11.31: 3
       11.31 -    15.08: 0
       15.08 -    18.85: 1
  Bond angle restraints: 3447
  Sorted by residual:
  angle pdb=" CA  LEU C 518 "
        pdb=" CB  LEU C 518 "
        pdb=" CG  LEU C 518 "
      ideal   model   delta    sigma   weight residual
     116.30  135.15  -18.85 3.50e+00 8.16e-02 2.90e+01
  angle pdb=" C   GLU H  33 "
        pdb=" N   MET H  34 "
        pdb=" CA  MET H  34 "
      ideal   model   delta    sigma   weight residual
     122.87  118.15    4.72 1.61e+00 3.86e-01 8.60e+00
  angle pdb=" C   LEU C 517 "
        pdb=" N   LEU C 518 "
        pdb=" CA  LEU C 518 "
      ideal   model   delta    sigma   weight residual
     122.68  126.77   -4.09 1.47e+00 4.63e-01 7.72e+00
  angle pdb=" CA  TYR C 495 "
        pdb=" CB  TYR C 495 "
        pdb=" CG  TYR C 495 "
      ideal   model   delta    sigma   weight residual
     113.90  118.77   -4.87 1.80e+00 3.09e-01 7.31e+00
  angle pdb=" CA  TYR C 473 "
        pdb=" CB  TYR C 473 "
        pdb=" CG  TYR C 473 "
      ideal   model   delta    sigma   weight residual
     113.90  118.55   -4.65 1.80e+00 3.09e-01 6.69e+00
  ... (remaining 3442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.12: 1332
       15.12 -    30.23: 130
       30.23 -    45.35: 23
       45.35 -    60.47: 3
       60.47 -    75.58: 2
  Dihedral angle restraints: 1490
    sinusoidal: 589
      harmonic: 901
  Sorted by residual:
  dihedral pdb=" CA  ALA C 520 "
           pdb=" C   ALA C 520 "
           pdb=" N   PRO C 521 "
           pdb=" CA  PRO C 521 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.25   20.75     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  LEU C 517 "
           pdb=" C   LEU C 517 "
           pdb=" N   LEU C 518 "
           pdb=" CA  LEU C 518 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.50   20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  95 "
           pdb=" CB  CYS H  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.46   30.54     1      1.00e+01 1.00e-02 1.33e+01
  ... (remaining 1487 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 207
       0.038 -    0.077: 95
       0.077 -    0.115: 37
       0.115 -    0.154: 22
       0.154 -    0.192: 3
  Chirality restraints: 364
  Sorted by residual:
  chirality pdb=" CA  ILE C 434 "
            pdb=" N   ILE C 434 "
            pdb=" C   ILE C 434 "
            pdb=" CB  ILE C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.22e-01
  chirality pdb=" CA  LEU C 518 "
            pdb=" N   LEU C 518 "
            pdb=" C   LEU C 518 "
            pdb=" CB  LEU C 518 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" CB  THR H  90 "
            pdb=" CA  THR H  90 "
            pdb=" OG1 THR H  90 "
            pdb=" CG2 THR H  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.76e-01
  ... (remaining 361 not shown)

  Planarity restraints: 448
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 520 "   -0.038 5.00e-02 4.00e+02   5.69e-02 5.18e+00
        pdb=" N   PRO C 521 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO C 521 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 521 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 462 "    0.036 5.00e-02 4.00e+02   5.40e-02 4.66e+00
        pdb=" N   PRO C 463 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 463 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 463 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 362 "   -0.009 2.00e-02 2.50e+03   1.90e-02 3.62e+00
        pdb=" C   VAL C 362 "    0.033 2.00e-02 2.50e+03
        pdb=" O   VAL C 362 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA C 363 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 445 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 757
        2.82 -     3.34: 1959
        3.34 -     3.86: 4099
        3.86 -     4.38: 4610
        4.38 -     4.90: 8120
  Nonbonded interactions: 19545
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 359 "
            pdb=" OD1 ASN C 394 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   ASN C 481 "
            pdb=" NE2 GLN H  39 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" OD1 ASP C 442 "
            pdb=" OH  TYR C 451 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" NH2 ARG C 454 "
            pdb=" O   ASP C 467 "
     model   vdw
     2.390 3.120
  nonbonded pdb=" OG  SER H 117 "
            pdb=" N   SER H 118 "
     model   vdw
     2.392 3.120
  ... (remaining 19540 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.610
  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:             0.010
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.760
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.000
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
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   0.049   2540  Z= 0.266
  Angle     :  0.954  18.847   3460  Z= 0.483
  Chirality :  0.057   0.192    364
  Planarity :  0.007   0.057    447
  Dihedral  : 12.401  75.582    907
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  1.51 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.41), residues: 307
  helix: -4.35 (0.46), residues: 33
  sheet:  0.00 (0.51), residues: 90
  loop : -1.97 (0.37), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 355 
 TYR   0.028   0.003   TYR C 495 
 PHE   0.032   0.004   PHE C 347 
 TRP   0.012   0.002   TRP C 436 
 HIS   0.001   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00606 ( 2534)
  covalent geometry    : angle       0.95118 ( 3447)
  SS BOND              : bond        0.00324 (    5)
  SS BOND              : angle       1.25721 (   10)
  hydrogen bonds       : bond        0.17742 (   75)
  hydrogen bonds       : angle       9.94340 (  204)
  link_NAG-ASN         : bond        0.00313 (    1)
  link_NAG-ASN         : angle       1.96518 (    3)

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

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

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: C  386 LYS cc_start: 0.8480 (mmtp) cc_final: 0.7349 (ttpt)
REVERT: H   20 LEU cc_start: 0.8405 (mt) cc_final: 0.8196 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0886
  time to fit residues: 8.3742
Evaluate side-chains
  67 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C 437 ASN
C 481 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.111722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.094443 restraints weight = 4312.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.94
r_work: 0.3115 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2540  Z= 0.210
  Angle     :  0.647  11.465   3460  Z= 0.332
  Chirality :  0.044   0.158    364
  Planarity :  0.005   0.039    447
  Dihedral  :  5.679  26.408    369
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 10.57 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.43), residues: 307
  helix: -3.47 (0.61), residues: 34
  sheet:  0.15 (0.53), residues: 90
  loop : -1.73 (0.40), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 457 
 TYR   0.021   0.001   TYR C 495 
 PHE   0.015   0.002   PHE C 347 
 TRP   0.010   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 2534)
  covalent geometry    : angle       0.64510 ( 3447)
  SS BOND              : bond        0.00171 (    5)
  SS BOND              : angle       0.65477 (   10)
  hydrogen bonds       : bond        0.03922 (   75)
  hydrogen bonds       : angle       7.41449 (  204)
  link_NAG-ASN         : bond        0.00418 (    1)
  link_NAG-ASN         : angle       1.85311 (    3)

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

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

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.102 
Fit side-chains
REVERT: C  386 LYS cc_start: 0.8495 (mmtp) cc_final: 0.7385 (ttpt)
REVERT: C  403 ARG cc_start: 0.8726 (ptt180) cc_final: 0.8298 (ptt180)
REVERT: H   22 CYS cc_start: 0.7194 (t) cc_final: 0.6960 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 83
  average time/residue: 0.0855
  time to fit residues: 7.9646
Evaluate side-chains
  73 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue  112 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 28 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.111497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.093768 restraints weight = 4406.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 3.07
r_work: 0.3119 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2540  Z= 0.174
  Angle     :  0.600  10.175   3460  Z= 0.306
  Chirality :  0.044   0.147    364
  Planarity :  0.004   0.034    447
  Dihedral  :  5.232  25.644    369
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.96 %
    Favored  : 83.77 %
  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 are not related in a simple way.
  whole: -1.67 (0.45), residues: 307
  helix: -3.06 (0.78), residues: 34
  sheet:  0.41 (0.53), residues: 90
  loop : -1.57 (0.42), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  66 
 TYR   0.020   0.001   TYR C 495 
 PHE   0.010   0.001   PHE C 347 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 2534)
  covalent geometry    : angle       0.59872 ( 3447)
  SS BOND              : bond        0.00171 (    5)
  SS BOND              : angle       0.48755 (   10)
  hydrogen bonds       : bond        0.03543 (   75)
  hydrogen bonds       : angle       6.86546 (  204)
  link_NAG-ASN         : bond        0.00369 (    1)
  link_NAG-ASN         : angle       1.74006 (    3)

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

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

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.093 
Fit side-chains
REVERT: C  378 LYS cc_start: 0.8810 (mttm) cc_final: 0.8568 (mtpp)
REVERT: C  386 LYS cc_start: 0.8499 (mmtp) cc_final: 0.7349 (ttpt)
REVERT: C  501 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8597 (m-10)
REVERT: H   22 CYS cc_start: 0.7219 (t) cc_final: 0.6964 (t)
REVERT: H   79 TYR cc_start: 0.8021 (m-10) cc_final: 0.7598 (m-10)
  outliers start: 6
  outliers final: 3
  residues processed: 78
  average time/residue: 0.0995
  time to fit residues: 8.6432
Evaluate side-chains
  76 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  501 TYR
Chi-restraints excluded: chain H residue  112 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.110296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.092826 restraints weight = 4353.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 3.03
r_work: 0.3100 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2540  Z= 0.184
  Angle     :  0.584   9.050   3460  Z= 0.301
  Chirality :  0.043   0.143    364
  Planarity :  0.004   0.034    447
  Dihedral  :  5.152  25.272    369
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 13.96 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.46), residues: 307
  helix: -3.04 (0.80), residues: 34
  sheet:  0.61 (0.54), residues: 88
  loop : -1.48 (0.43), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 408 
 TYR   0.020   0.001   TYR C 495 
 PHE   0.011   0.001   PHE C 347 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 2534)
  covalent geometry    : angle       0.58273 ( 3447)
  SS BOND              : bond        0.00195 (    5)
  SS BOND              : angle       0.48698 (   10)
  hydrogen bonds       : bond        0.03387 (   75)
  hydrogen bonds       : angle       6.63771 (  204)
  link_NAG-ASN         : bond        0.00350 (    1)
  link_NAG-ASN         : angle       1.60187 (    3)

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

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

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.091 
Fit side-chains
REVERT: C  378 LYS cc_start: 0.8793 (mttm) cc_final: 0.8525 (mtpp)
REVERT: C  386 LYS cc_start: 0.8494 (mmtp) cc_final: 0.7349 (ttpt)
REVERT: C  481 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7758 (t0)
REVERT: H   22 CYS cc_start: 0.7223 (t) cc_final: 0.6958 (t)
REVERT: H   72 ASP cc_start: 0.8460 (t0) cc_final: 0.8013 (t0)
REVERT: H   79 TYR cc_start: 0.7981 (m-10) cc_final: 0.7569 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0869
  time to fit residues: 7.9803
Evaluate side-chains
  81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  481 ASN
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  112 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.110434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.092971 restraints weight = 4368.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 3.02
r_work: 0.3101 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2540  Z= 0.174
  Angle     :  0.572   8.371   3460  Z= 0.297
  Chirality :  0.044   0.139    364
  Planarity :  0.004   0.034    447
  Dihedral  :  5.123  25.294    369
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.96 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.46), residues: 307
  helix: -3.05 (0.80), residues: 34
  sheet:  0.57 (0.53), residues: 88
  loop : -1.39 (0.44), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  66 
 TYR   0.019   0.001   TYR C 495 
 PHE   0.012   0.001   PHE C 456 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 2534)
  covalent geometry    : angle       0.57030 ( 3447)
  SS BOND              : bond        0.00258 (    5)
  SS BOND              : angle       0.48133 (   10)
  hydrogen bonds       : bond        0.03346 (   75)
  hydrogen bonds       : angle       6.56579 (  204)
  link_NAG-ASN         : bond        0.00335 (    1)
  link_NAG-ASN         : angle       1.63017 (    3)

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

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

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.059 
Fit side-chains
REVERT: C  378 LYS cc_start: 0.8796 (mttm) cc_final: 0.8526 (mtpp)
REVERT: C  386 LYS cc_start: 0.8522 (mmtp) cc_final: 0.7459 (ttpt)
REVERT: C  403 ARG cc_start: 0.8654 (ptt180) cc_final: 0.8426 (ptt180)
REVERT: H   22 CYS cc_start: 0.7289 (t) cc_final: 0.7031 (t)
REVERT: H   72 ASP cc_start: 0.8472 (t0) cc_final: 0.8037 (t0)
REVERT: H   79 TYR cc_start: 0.7980 (m-10) cc_final: 0.7623 (m-10)
  outliers start: 8
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0939
  time to fit residues: 8.2996
Evaluate side-chains
  77 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  112 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 9 optimal weight:    0.2980
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.109954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.092612 restraints weight = 4359.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.98
r_work: 0.3098 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   2540  Z= 0.183
  Angle     :  0.569   7.875   3460  Z= 0.297
  Chirality :  0.043   0.138    364
  Planarity :  0.004   0.035    447
  Dihedral  :  5.129  25.457    369
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.85 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.46), residues: 307
  helix: -3.13 (0.78), residues: 34
  sheet:  0.55 (0.52), residues: 88
  loop : -1.31 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 355 
 TYR   0.019   0.001   TYR C 495 
 PHE   0.010   0.002   PHE C 347 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 2534)
  covalent geometry    : angle       0.56722 ( 3447)
  SS BOND              : bond        0.00173 (    5)
  SS BOND              : angle       0.42899 (   10)
  hydrogen bonds       : bond        0.03324 (   75)
  hydrogen bonds       : angle       6.49292 (  204)
  link_NAG-ASN         : bond        0.00354 (    1)
  link_NAG-ASN         : angle       1.64977 (    3)

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

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

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.089 
Fit side-chains
REVERT: C  378 LYS cc_start: 0.8796 (mttm) cc_final: 0.8513 (mtpt)
REVERT: C  386 LYS cc_start: 0.8522 (mmtp) cc_final: 0.7466 (ttpt)
REVERT: C  403 ARG cc_start: 0.8619 (ptt180) cc_final: 0.8348 (ptt180)
REVERT: C  405 ASP cc_start: 0.8334 (p0) cc_final: 0.8115 (p0)
REVERT: H   22 CYS cc_start: 0.7292 (t) cc_final: 0.7041 (t)
REVERT: H   72 ASP cc_start: 0.8432 (t0) cc_final: 0.7998 (t0)
REVERT: H   79 TYR cc_start: 0.7960 (m-10) cc_final: 0.7603 (m-10)
  outliers start: 7
  outliers final: 5
  residues processed: 81
  average time/residue: 0.0929
  time to fit residues: 8.3836
Evaluate side-chains
  77 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  112 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0050
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.111731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.094295 restraints weight = 4324.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 3.01
r_work: 0.3124 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2540  Z= 0.136
  Angle     :  0.546   7.596   3460  Z= 0.285
  Chirality :  0.043   0.136    364
  Planarity :  0.004   0.036    447
  Dihedral  :  4.901  24.531    369
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.60 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.47), residues: 307
  helix: -3.08 (0.93), residues: 27
  sheet:  0.76 (0.54), residues: 82
  loop : -1.30 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  66 
 TYR   0.018   0.001   TYR C 473 
 PHE   0.013   0.001   PHE C 456 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 2534)
  covalent geometry    : angle       0.54447 ( 3447)
  SS BOND              : bond        0.00164 (    5)
  SS BOND              : angle       0.36729 (   10)
  hydrogen bonds       : bond        0.03109 (   75)
  hydrogen bonds       : angle       6.36560 (  204)
  link_NAG-ASN         : bond        0.00285 (    1)
  link_NAG-ASN         : angle       1.58259 (    3)

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

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

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.095 
Fit side-chains
REVERT: C  378 LYS cc_start: 0.8792 (mttm) cc_final: 0.8495 (mtpt)
REVERT: C  386 LYS cc_start: 0.8491 (mmtp) cc_final: 0.7480 (ttpt)
REVERT: C  403 ARG cc_start: 0.8640 (ptt180) cc_final: 0.8382 (ptt180)
REVERT: C  405 ASP cc_start: 0.8333 (p0) cc_final: 0.8121 (p0)
REVERT: H   22 CYS cc_start: 0.7220 (t) cc_final: 0.6980 (t)
REVERT: H   66 ARG cc_start: 0.8601 (mtm110) cc_final: 0.8353 (mtm110)
REVERT: H   72 ASP cc_start: 0.8389 (t0) cc_final: 0.7968 (t0)
REVERT: H   79 TYR cc_start: 0.7969 (m-10) cc_final: 0.7618 (m-10)
  outliers start: 5
  outliers final: 4
  residues processed: 85
  average time/residue: 0.0958
  time to fit residues: 9.1174
Evaluate side-chains
  83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  112 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.110177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.092562 restraints weight = 4419.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 3.04
r_work: 0.3095 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2540  Z= 0.193
  Angle     :  0.595   7.861   3460  Z= 0.308
  Chirality :  0.045   0.165    364
  Planarity :  0.004   0.037    447
  Dihedral  :  5.079  24.696    369
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.49 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.46), residues: 307
  helix: -3.18 (0.77), residues: 34
  sheet:  0.47 (0.52), residues: 88
  loop : -1.25 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  66 
 TYR   0.019   0.002   TYR C 495 
 PHE   0.009   0.002   PHE C 347 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 2534)
  covalent geometry    : angle       0.59329 ( 3447)
  SS BOND              : bond        0.00156 (    5)
  SS BOND              : angle       0.47310 (   10)
  hydrogen bonds       : bond        0.03353 (   75)
  hydrogen bonds       : angle       6.42755 (  204)
  link_NAG-ASN         : bond        0.00335 (    1)
  link_NAG-ASN         : angle       1.62938 (    3)

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

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

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.096 
Fit side-chains
REVERT: C  378 LYS cc_start: 0.8794 (mttm) cc_final: 0.8507 (mtpt)
REVERT: C  386 LYS cc_start: 0.8558 (mmtp) cc_final: 0.7451 (ttpt)
REVERT: C  403 ARG cc_start: 0.8646 (ptt180) cc_final: 0.8380 (ptt180)
REVERT: C  405 ASP cc_start: 0.8389 (p0) cc_final: 0.8166 (p0)
REVERT: H   17 SER cc_start: 0.8435 (p) cc_final: 0.7935 (m)
REVERT: H   22 CYS cc_start: 0.7303 (t) cc_final: 0.7048 (t)
REVERT: H   72 ASP cc_start: 0.8370 (t0) cc_final: 0.7959 (t0)
REVERT: H   79 TYR cc_start: 0.7958 (m-10) cc_final: 0.7622 (m-10)
  outliers start: 8
  outliers final: 6
  residues processed: 80
  average time/residue: 0.1022
  time to fit residues: 9.0845
Evaluate side-chains
  80 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  112 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 11 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:
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.109591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.091950 restraints weight = 4449.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 3.05
r_work: 0.3087 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   2540  Z= 0.207
  Angle     :  0.601   7.774   3460  Z= 0.312
  Chirality :  0.045   0.161    364
  Planarity :  0.004   0.033    447
  Dihedral  :  5.206  25.823    369
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.36 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.46), residues: 307
  helix: -3.21 (0.75), residues: 34
  sheet:  0.43 (0.53), residues: 88
  loop : -1.27 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  66 
 TYR   0.019   0.002   TYR C 495 
 PHE   0.011   0.002   PHE C 456 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.001   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 2534)
  covalent geometry    : angle       0.59970 ( 3447)
  SS BOND              : bond        0.00159 (    5)
  SS BOND              : angle       0.48459 (   10)
  hydrogen bonds       : bond        0.03385 (   75)
  hydrogen bonds       : angle       6.47845 (  204)
  link_NAG-ASN         : bond        0.00310 (    1)
  link_NAG-ASN         : angle       1.74607 (    3)

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

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

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.088 
Fit side-chains
REVERT: C  378 LYS cc_start: 0.8800 (mttm) cc_final: 0.8514 (mtpt)
REVERT: C  386 LYS cc_start: 0.8522 (mmtp) cc_final: 0.7483 (ttpt)
REVERT: H   17 SER cc_start: 0.8342 (p) cc_final: 0.7835 (m)
REVERT: H   22 CYS cc_start: 0.7324 (t) cc_final: 0.7073 (t)
REVERT: H   72 ASP cc_start: 0.8354 (t0) cc_final: 0.7942 (t0)
REVERT: H   79 TYR cc_start: 0.7974 (m-10) cc_final: 0.7618 (m-10)
  outliers start: 10
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1003
  time to fit residues: 8.7029
Evaluate side-chains
  80 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  112 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0170
   chunk 4 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0050
   chunk 6 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.4032

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

Flipped N/Q/H residues before XYZ refinement:
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.112153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.094519 restraints weight = 4431.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 3.05
r_work: 0.3129 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2540  Z= 0.131
  Angle     :  0.568   7.745   3460  Z= 0.294
  Chirality :  0.043   0.135    364
  Planarity :  0.003   0.037    447
  Dihedral  :  4.942  24.800    369
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.00 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.47), residues: 307
  helix: -3.11 (0.92), residues: 27
  sheet:  0.72 (0.55), residues: 82
  loop : -1.25 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  66 
 TYR   0.017   0.001   TYR C 473 
 PHE   0.007   0.001   PHE H  29 
 TRP   0.010   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2534)
  covalent geometry    : angle       0.56707 ( 3447)
  SS BOND              : bond        0.00119 (    5)
  SS BOND              : angle       0.30707 (   10)
  hydrogen bonds       : bond        0.03110 (   75)
  hydrogen bonds       : angle       6.33027 (  204)
  link_NAG-ASN         : bond        0.00288 (    1)
  link_NAG-ASN         : angle       1.61020 (    3)

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

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

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  614 Ramachandran restraints generated.
    307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.091 
Fit side-chains
REVERT: C  378 LYS cc_start: 0.8787 (mttm) cc_final: 0.8499 (mtpt)
REVERT: C  386 LYS cc_start: 0.8441 (mmtp) cc_final: 0.7362 (ttpt)
REVERT: H   17 SER cc_start: 0.8444 (p) cc_final: 0.7992 (m)
REVERT: H   22 CYS cc_start: 0.7231 (t) cc_final: 0.6981 (t)
REVERT: H   72 ASP cc_start: 0.8338 (t0) cc_final: 0.7967 (t0)
REVERT: H   81 GLN cc_start: 0.8097 (tt0) cc_final: 0.7787 (tt0)
REVERT: H  113 LEU cc_start: 0.8796 (tt) cc_final: 0.8534 (mp)
  outliers start: 6
  outliers final: 5
  residues processed: 79
  average time/residue: 0.0974
  time to fit residues: 8.6189
Evaluate side-chains
  81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue  112 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 14 optimal weight:    0.0980
   chunk 24 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.111333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.093773 restraints weight = 4439.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 3.00
r_work: 0.3119 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2540  Z= 0.166
  Angle     :  0.580   7.654   3460  Z= 0.302
  Chirality :  0.044   0.136    364
  Planarity :  0.004   0.038    447
  Dihedral  :  5.028  24.327    369
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 20.38 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.46), residues: 307
  helix: -3.10 (0.91), residues: 27
  sheet:  0.61 (0.54), residues: 82
  loop : -1.27 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  19 
 TYR   0.018   0.001   TYR C 495 
 PHE   0.012   0.002   PHE C 456 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 2534)
  covalent geometry    : angle       0.57853 ( 3447)
  SS BOND              : bond        0.00130 (    5)
  SS BOND              : angle       0.39394 (   10)
  hydrogen bonds       : bond        0.03263 (   75)
  hydrogen bonds       : angle       6.34533 (  204)
  link_NAG-ASN         : bond        0.00314 (    1)
  link_NAG-ASN         : angle       1.63107 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 871.42 seconds
wall clock time: 15 minutes 28.27 seconds (928.27 seconds total)