Starting phenix.real_space_refine
on Wed Jul 23 07:47:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jzm_22533/07_2025/7jzm_22533.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jzm_22533/07_2025/7jzm_22533.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jzm_22533/07_2025/7jzm_22533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jzm_22533/07_2025/7jzm_22533.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jzm_22533/07_2025/7jzm_22533.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jzm_22533/07_2025/7jzm_22533.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.022
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      10      5.16       5
     C    1310      2.51       5
     N     340      2.21       5
     O     373      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 2033
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 495
          Classifications: {'peptide': 64}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'TRANS': 63}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 40
    Chain: "B"
      Number of atoms: 1500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1500
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.10, per 1000 atoms: 1.52
  Number of scatterers: 2033
  At special positions: 0
  Unit cell: (66.15, 68.25, 69.3, 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      10     16.00
     O     373      8.00
     N     340      7.00
     C    1310      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.28
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    BETA1-6
      " NAG C   1 " - " FUC C   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG C   1 " - " ASN B 343 "
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 297.2 milliseconds
  

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  486

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 4 sheets defined
      38.4% alpha, 15.9% 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 1 through 17
    Processing helix  chain 'A' and resid 22 through 42
    Processing helix  chain 'A' and resid 44 through 64
    Processing helix  chain 'B' and resid 337 through 341
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.804A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 389
      removed outlier: 3.514A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.158A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.670A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.479A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474

    93 hydrogen bonds defined for protein.
    240 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: 0.52

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 591
        1.33 -     1.46: 586
        1.46 -     1.59: 893
        1.59 -     1.72: 0
        1.72 -     1.85: 12
  Bond restraints: 2082
  Sorted by residual:
  bond pdb=" N   PRO B 499 "
       pdb=" CD  PRO B 499 "
    ideal  model  delta    sigma   weight residual
    1.473  1.337  0.136 1.40e-02 5.10e+03 9.45e+01
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.479 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" CG  GLN B 506 "
       pdb=" CD  GLN B 506 "
    ideal  model  delta    sigma   weight residual
    1.516  1.438  0.078 2.50e-02 1.60e+03 9.74e+00
  bond pdb=" C5  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.38e+00
  bond pdb=" C5  FUC C   3 "
       pdb=" O5  FUC C   3 "
    ideal  model  delta    sigma   weight residual
    1.423  1.477 -0.054 2.00e-02 2.50e+03 7.29e+00
  ... (remaining 2077 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 2649
        2.56 -     5.12: 157
        5.12 -     7.69: 20
        7.69 -    10.25: 3
       10.25 -    12.81: 1
  Bond angle restraints: 2830
  Sorted by residual:
  angle pdb=" N   PRO B 499 "
        pdb=" CA  PRO B 499 "
        pdb=" CB  PRO B 499 "
      ideal   model   delta    sigma   weight residual
     103.41   96.76    6.65 9.40e-01 1.13e+00 5.01e+01
  angle pdb=" CA  PRO B 499 "
        pdb=" N   PRO B 499 "
        pdb=" CD  PRO B 499 "
      ideal   model   delta    sigma   weight residual
     112.00  120.93   -8.93 1.40e+00 5.10e-01 4.07e+01
  angle pdb=" C   ALA B 520 "
        pdb=" N   PRO B 521 "
        pdb=" CA  PRO B 521 "
      ideal   model   delta    sigma   weight residual
     119.56  126.01   -6.45 1.02e+00 9.61e-01 4.00e+01
  angle pdb=" C   GLN B 498 "
        pdb=" N   PRO B 499 "
        pdb=" CA  PRO B 499 "
      ideal   model   delta    sigma   weight residual
     119.87  126.31   -6.44 1.04e+00 9.25e-01 3.84e+01
  angle pdb=" C   PHE B 490 "
        pdb=" N   PRO B 491 "
        pdb=" CA  PRO B 491 "
      ideal   model   delta    sigma   weight residual
     119.56  125.65   -6.09 1.01e+00 9.80e-01 3.64e+01
  ... (remaining 2825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.30: 1208
       14.30 -    28.59: 48
       28.59 -    42.89: 8
       42.89 -    57.18: 5
       57.18 -    71.48: 3
  Dihedral angle restraints: 1272
    sinusoidal: 513
      harmonic: 759
  Sorted by residual:
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.36   41.64     1      1.00e+01 1.00e-02 2.43e+01
  dihedral pdb=" CB  GLU B 484 "
           pdb=" CG  GLU B 484 "
           pdb=" CD  GLU B 484 "
           pdb=" OE1 GLU B 484 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   71.48  -71.48     1      3.00e+01 1.11e-03 7.28e+00
  dihedral pdb=" CA  ALA B 520 "
           pdb=" C   ALA B 520 "
           pdb=" N   PRO B 521 "
           pdb=" CA  PRO B 521 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.92   13.08     0      5.00e+00 4.00e-02 6.85e+00
  ... (remaining 1269 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 230
       0.082 -    0.164: 69
       0.164 -    0.245: 15
       0.245 -    0.327: 3
       0.327 -    0.409: 1
  Chirality restraints: 318
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.59    0.19 2.00e-02 2.50e+03 9.38e+01
  chirality pdb=" C1  FUC C   3 "
            pdb=" O6  NAG C   1 "
            pdb=" C2  FUC C   3 "
            pdb=" O5  FUC C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.48    0.08 2.00e-02 2.50e+03 1.68e+01
  chirality pdb=" C2  NAG C   2 "
            pdb=" C1  NAG C   2 "
            pdb=" C3  NAG C   2 "
            pdb=" N2  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.90    0.41 2.00e-01 2.50e+01 4.18e+00
  ... (remaining 315 not shown)

  Planarity restraints: 364
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "    0.036 2.00e-02 2.50e+03   1.86e-02 6.92e+00
        pdb=" CG  TYR B 495 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 453 "    0.025 2.00e-02 2.50e+03   1.34e-02 3.57e+00
        pdb=" CG  TYR B 453 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 453 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 453 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 453 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 453 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 453 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B 453 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 343 "   -0.016 2.00e-02 2.50e+03   1.65e-02 3.40e+00
        pdb=" CG  ASN B 343 "    0.007 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 343 "    0.004 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 343 "    0.025 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 361 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 880
        2.92 -     3.41: 1816
        3.41 -     3.91: 3445
        3.91 -     4.40: 3881
        4.40 -     4.90: 6261
  Nonbonded interactions: 16283
  Sorted by model distance:
  nonbonded pdb=" O   ASP A   2 "
            pdb=" OD1 ASP A   2 "
     model   vdw
     2.420 3.040
  nonbonded pdb=" N   ASP B 428 "
            pdb=" OD1 ASP B 428 "
     model   vdw
     2.566 3.120
  nonbonded pdb=" O   ASN B 501 "
            pdb=" NE2 GLN B 506 "
     model   vdw
     2.568 3.120
  nonbonded pdb=" O5  NAG C   1 "
            pdb=" O6  NAG C   1 "
     model   vdw
     2.569 2.432
  nonbonded pdb=" N   SER B 373 "
            pdb=" N   PHE B 374 "
     model   vdw
     2.574 2.560
  ... (remaining 16278 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 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:             3.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     12.230
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
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      :  0.016   0.245   2089  Z= 0.861
  Angle     :  1.414  12.996   2847  Z= 0.931
  Chirality :  0.084   0.409    318
  Planarity :  0.005   0.026    363
  Dihedral  :  9.533  71.478    774
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.52), residues: 254
  helix:  0.21 (0.51), residues: 85
  sheet:  0.78 (0.76), residues: 52
  loop :  0.82 (0.60), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.005   TRP B 353 
 HIS   0.002   0.001   HIS A   6 
 PHE   0.013   0.002   PHE B 342 
 TYR   0.036   0.006   TYR B 495 
 ARG   0.003   0.000   ARG B 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05758 (    1)
  link_NAG-ASN         : angle       2.63632 (    3)
  link_BETA1-4         : bond        0.07488 (    1)
  link_BETA1-4         : angle       3.76318 (    3)
  hydrogen bonds       : bond        0.15984 (   93)
  hydrogen bonds       : angle       7.20776 (  240)
  link_BETA1-6         : bond        0.05859 (    1)
  link_BETA1-6         : angle       2.72093 (    3)
  SS BOND              : bond        0.12244 (    4)
  SS BOND              : angle       5.43319 (    8)
  covalent geometry    : bond        0.01477 ( 2082)
  covalent geometry    : angle       1.37761 ( 2830)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.248 
Fit side-chains
REVERT: B  469 SER cc_start: 0.8421 (t) cc_final: 0.7854 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1809
  time to fit residues: 13.4610
Evaluate side-chains
  42 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 18 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0980
   chunk 6 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0970
   chunk 19 optimal weight:    0.5980
   chunk 7 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0040
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0980
   overall best weight:    0.1390

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.133113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.117624 restraints weight = 2933.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.120576 restraints weight = 1580.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.122583 restraints weight = 1055.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2089  Z= 0.139
  Angle     :  0.634   7.725   2847  Z= 0.329
  Chirality :  0.043   0.145    318
  Planarity :  0.004   0.039    363
  Dihedral  :  6.053  57.400    344
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.45 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.53), residues: 254
  helix:  1.00 (0.58), residues: 88
  sheet:  0.57 (0.78), residues: 49
  loop :  0.57 (0.57), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 436 
 HIS   0.002   0.001   HIS A   6 
 PHE   0.015   0.002   PHE A  33 
 TYR   0.017   0.002   TYR B 495 
 ARG   0.002   0.001   ARG A  45 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00221 (    1)
  link_NAG-ASN         : angle       1.15852 (    3)
  link_BETA1-4         : bond        0.00042 (    1)
  link_BETA1-4         : angle       1.32804 (    3)
  hydrogen bonds       : bond        0.05159 (   93)
  hydrogen bonds       : angle       5.23993 (  240)
  link_BETA1-6         : bond        0.00746 (    1)
  link_BETA1-6         : angle       1.23418 (    3)
  SS BOND              : bond        0.00666 (    4)
  SS BOND              : angle       1.53051 (    8)
  covalent geometry    : bond        0.00286 ( 2082)
  covalent geometry    : angle       0.62678 ( 2830)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 ILE cc_start: 0.8287 (mm) cc_final: 0.7854 (mt)
  outliers start: 4
  outliers final: 2
  residues processed: 40
  average time/residue: 0.1783
  time to fit residues: 8.2694
Evaluate side-chains
  40 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 19 optimal weight:    0.0770
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 12 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 6 optimal weight:    0.0970
   chunk 15 optimal weight:    0.2980
   chunk 13 optimal weight:    0.3980
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    0.7980
   overall best weight:    0.2536

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

Flipped N/Q/H residues before XYZ refinement:
A   6 HIS
A  43 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.127817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.111485 restraints weight = 2958.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.114422 restraints weight = 1630.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.116336 restraints weight = 1101.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2089  Z= 0.168
  Angle     :  0.582   6.003   2847  Z= 0.302
  Chirality :  0.042   0.142    318
  Planarity :  0.004   0.039    363
  Dihedral  :  6.126  58.971    344
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  8.96 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.53), residues: 254
  helix:  1.03 (0.57), residues: 89
  sheet:  0.05 (0.74), residues: 49
  loop :  0.38 (0.57), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 436 
 HIS   0.001   0.001   HIS A  18 
 PHE   0.009   0.001   PHE B 429 
 TYR   0.016   0.002   TYR B 495 
 ARG   0.002   0.000   ARG A  45 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00032 (    1)
  link_NAG-ASN         : angle       1.19463 (    3)
  link_BETA1-4         : bond        0.00432 (    1)
  link_BETA1-4         : angle       1.05202 (    3)
  hydrogen bonds       : bond        0.04477 (   93)
  hydrogen bonds       : angle       5.02520 (  240)
  link_BETA1-6         : bond        0.00824 (    1)
  link_BETA1-6         : angle       1.56986 (    3)
  SS BOND              : bond        0.00564 (    4)
  SS BOND              : angle       1.50782 (    8)
  covalent geometry    : bond        0.00365 ( 2082)
  covalent geometry    : angle       0.57412 ( 2830)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.8449 (mm) cc_final: 0.8066 (mt)
REVERT: A   34 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7644 (mp0)
REVERT: B  489 TYR cc_start: 0.7934 (m-80) cc_final: 0.7098 (m-80)
  outliers start: 4
  outliers final: 3
  residues processed: 43
  average time/residue: 0.1421
  time to fit residues: 7.2490
Evaluate side-chains
  38 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 0 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0980
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0970
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0870
   chunk 13 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0970
   overall best weight:    0.1354

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

Flipped N/Q/H residues before XYZ refinement:
B 498 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.129396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.112935 restraints weight = 2935.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.115768 restraints weight = 1648.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.117684 restraints weight = 1126.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2089  Z= 0.115
  Angle     :  0.558   6.872   2847  Z= 0.282
  Chirality :  0.041   0.137    318
  Planarity :  0.003   0.040    363
  Dihedral  :  5.992  59.414    344
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 11.44 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.53), residues: 254
  helix:  1.14 (0.57), residues: 88
  sheet: -0.12 (0.73), residues: 49
  loop :  0.37 (0.57), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 436 
 HIS   0.001   0.001   HIS A   6 
 PHE   0.012   0.001   PHE A  33 
 TYR   0.010   0.001   TYR B 495 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00040 (    1)
  link_NAG-ASN         : angle       1.13115 (    3)
  link_BETA1-4         : bond        0.00363 (    1)
  link_BETA1-4         : angle       1.07873 (    3)
  hydrogen bonds       : bond        0.03885 (   93)
  hydrogen bonds       : angle       4.85394 (  240)
  link_BETA1-6         : bond        0.00809 (    1)
  link_BETA1-6         : angle       1.37579 (    3)
  SS BOND              : bond        0.00448 (    4)
  SS BOND              : angle       1.23348 (    8)
  covalent geometry    : bond        0.00244 ( 2082)
  covalent geometry    : angle       0.55195 ( 2830)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.8467 (mm) cc_final: 0.8106 (mt)
REVERT: A   34 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7615 (mt-10)
REVERT: B  489 TYR cc_start: 0.7791 (m-80) cc_final: 0.7082 (m-80)
  outliers start: 5
  outliers final: 4
  residues processed: 43
  average time/residue: 0.1511
  time to fit residues: 7.7572
Evaluate side-chains
  40 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 15 optimal weight:    0.1980
   chunk 14 optimal weight:    0.0870
   chunk 12 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0770
   chunk 21 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    0.4980
   chunk 20 optimal weight:    0.0980
   chunk 10 optimal weight:    0.0980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.1116

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

Flipped N/Q/H residues before XYZ refinement:
A  18 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.129536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.113013 restraints weight = 2966.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.115914 restraints weight = 1626.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.117868 restraints weight = 1099.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2089  Z= 0.105
  Angle     :  0.551   9.223   2847  Z= 0.274
  Chirality :  0.041   0.132    318
  Planarity :  0.004   0.041    363
  Dihedral  :  5.914  59.946    344
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 11.44 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.53), residues: 254
  helix:  1.20 (0.58), residues: 88
  sheet: -0.13 (0.73), residues: 49
  loop :  0.39 (0.58), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 436 
 HIS   0.001   0.001   HIS A  18 
 PHE   0.011   0.001   PHE A  33 
 TYR   0.009   0.001   TYR B 495 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00066 (    1)
  link_NAG-ASN         : angle       1.05997 (    3)
  link_BETA1-4         : bond        0.00438 (    1)
  link_BETA1-4         : angle       1.06058 (    3)
  hydrogen bonds       : bond        0.03698 (   93)
  hydrogen bonds       : angle       4.74568 (  240)
  link_BETA1-6         : bond        0.00707 (    1)
  link_BETA1-6         : angle       1.28757 (    3)
  SS BOND              : bond        0.00344 (    4)
  SS BOND              : angle       1.25474 (    8)
  covalent geometry    : bond        0.00218 ( 2082)
  covalent geometry    : angle       0.54471 ( 2830)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A    9 MET cc_start: 0.7846 (tmm) cc_final: 0.7626 (ttt)
REVERT: A   25 ILE cc_start: 0.8546 (mm) cc_final: 0.8186 (mt)
REVERT: A   34 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7600 (mt-10)
REVERT: B  489 TYR cc_start: 0.7746 (m-80) cc_final: 0.7022 (m-80)
  outliers start: 5
  outliers final: 3
  residues processed: 42
  average time/residue: 0.1426
  time to fit residues: 7.1228
Evaluate side-chains
  37 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0970
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0770
   chunk 11 optimal weight:    0.0980
   chunk 16 optimal weight:    0.0970
   chunk 22 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    0.1980
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.0932

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.130788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.113980 restraints weight = 2905.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.116850 restraints weight = 1614.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.118736 restraints weight = 1101.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   2089  Z= 0.103
  Angle     :  0.519   5.151   2847  Z= 0.269
  Chirality :  0.041   0.130    318
  Planarity :  0.004   0.043    363
  Dihedral  :  5.845  59.704    344
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 13.43 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.53), residues: 254
  helix:  1.23 (0.57), residues: 88
  sheet: -0.03 (0.76), residues: 49
  loop :  0.39 (0.58), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 436 
 HIS   0.001   0.000   HIS A   6 
 PHE   0.010   0.001   PHE A  33 
 TYR   0.008   0.001   TYR A  14 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00052 (    1)
  link_NAG-ASN         : angle       1.05647 (    3)
  link_BETA1-4         : bond        0.00369 (    1)
  link_BETA1-4         : angle       1.03246 (    3)
  hydrogen bonds       : bond        0.03441 (   93)
  hydrogen bonds       : angle       4.64393 (  240)
  link_BETA1-6         : bond        0.00822 (    1)
  link_BETA1-6         : angle       1.27325 (    3)
  SS BOND              : bond        0.00297 (    4)
  SS BOND              : angle       1.13135 (    8)
  covalent geometry    : bond        0.00218 ( 2082)
  covalent geometry    : angle       0.51271 ( 2830)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.8626 (mm) cc_final: 0.8259 (mt)
REVERT: A   34 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7619 (mt-10)
REVERT: A   59 LEU cc_start: 0.8904 (tp) cc_final: 0.8605 (tp)
REVERT: B  489 TYR cc_start: 0.7549 (m-80) cc_final: 0.6686 (m-80)
  outliers start: 6
  outliers final: 3
  residues processed: 36
  average time/residue: 0.1414
  time to fit residues: 6.0648
Evaluate side-chains
  35 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 5 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 3 optimal weight:    0.2980
   chunk 6 optimal weight:    0.1980
   chunk 22 optimal weight:    0.2980
   chunk 21 optimal weight:    0.0270
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0970
   overall best weight:    0.1836

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.129114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.112451 restraints weight = 2986.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.115262 restraints weight = 1691.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.117144 restraints weight = 1166.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   2089  Z= 0.131
  Angle     :  0.579   9.898   2847  Z= 0.290
  Chirality :  0.042   0.132    318
  Planarity :  0.003   0.043    363
  Dihedral  :  5.825  58.101    344
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 13.93 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.54), residues: 254
  helix:  1.17 (0.57), residues: 88
  sheet: -0.07 (0.78), residues: 49
  loop :  0.26 (0.57), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 436 
 HIS   0.002   0.001   HIS A   6 
 PHE   0.009   0.001   PHE B 464 
 TYR   0.010   0.001   TYR B 495 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00018 (    1)
  link_NAG-ASN         : angle       1.16577 (    3)
  link_BETA1-4         : bond        0.00388 (    1)
  link_BETA1-4         : angle       1.03049 (    3)
  hydrogen bonds       : bond        0.03533 (   93)
  hydrogen bonds       : angle       4.71329 (  240)
  link_BETA1-6         : bond        0.00803 (    1)
  link_BETA1-6         : angle       1.39266 (    3)
  SS BOND              : bond        0.00287 (    4)
  SS BOND              : angle       1.16832 (    8)
  covalent geometry    : bond        0.00290 ( 2082)
  covalent geometry    : angle       0.57355 ( 2830)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.8602 (mm) cc_final: 0.8236 (mt)
REVERT: A   34 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7641 (mp0)
REVERT: B  489 TYR cc_start: 0.7513 (m-80) cc_final: 0.6303 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 38
  average time/residue: 0.1353
  time to fit residues: 6.1681
Evaluate side-chains
  37 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  468 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 22 optimal weight:    0.0870
   chunk 14 optimal weight:    0.1980
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    0.2980
   chunk 16 optimal weight:    0.0970
   chunk 11 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 2 optimal weight:    0.1980
   chunk 10 optimal weight:    0.0970
   chunk 19 optimal weight:    0.0870
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.1132

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.130565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.113585 restraints weight = 3018.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.116567 restraints weight = 1673.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.118538 restraints weight = 1132.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   2089  Z= 0.107
  Angle     :  0.572   9.445   2847  Z= 0.282
  Chirality :  0.041   0.129    318
  Planarity :  0.003   0.043    363
  Dihedral  :  5.773  57.396    344
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 13.43 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.54), residues: 254
  helix:  1.15 (0.58), residues: 88
  sheet:  0.00 (0.80), residues: 49
  loop :  0.22 (0.58), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 436 
 HIS   0.000   0.000   HIS A   6 
 PHE   0.010   0.001   PHE B 464 
 TYR   0.008   0.001   TYR A  14 
 ARG   0.004   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00032 (    1)
  link_NAG-ASN         : angle       1.09148 (    3)
  link_BETA1-4         : bond        0.00368 (    1)
  link_BETA1-4         : angle       1.01575 (    3)
  hydrogen bonds       : bond        0.03329 (   93)
  hydrogen bonds       : angle       4.67351 (  240)
  link_BETA1-6         : bond        0.00776 (    1)
  link_BETA1-6         : angle       1.29039 (    3)
  SS BOND              : bond        0.00387 (    4)
  SS BOND              : angle       1.15270 (    8)
  covalent geometry    : bond        0.00232 ( 2082)
  covalent geometry    : angle       0.56645 ( 2830)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A    9 MET cc_start: 0.7746 (tmm) cc_final: 0.7363 (ttp)
REVERT: A   25 ILE cc_start: 0.8627 (mm) cc_final: 0.8258 (mt)
REVERT: A   34 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7585 (mp0)
REVERT: A   59 LEU cc_start: 0.8863 (tp) cc_final: 0.8580 (tp)
REVERT: B  489 TYR cc_start: 0.7358 (m-80) cc_final: 0.6224 (m-80)
  outliers start: 6
  outliers final: 5
  residues processed: 38
  average time/residue: 0.1289
  time to fit residues: 5.9505
Evaluate side-chains
  39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 3 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    0.1980
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0050
   chunk 12 optimal weight:    0.4980
   chunk 24 optimal weight:    0.5980
   chunk 8 optimal weight:    0.1980
   chunk 5 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.2194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.128344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.111782 restraints weight = 3098.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.114634 restraints weight = 1749.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.116501 restraints weight = 1197.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   2089  Z= 0.153
  Angle     :  0.637  14.453   2847  Z= 0.310
  Chirality :  0.043   0.175    318
  Planarity :  0.004   0.044    363
  Dihedral  :  5.758  55.682    344
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 13.43 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.54), residues: 254
  helix:  1.13 (0.58), residues: 88
  sheet: -0.13 (0.80), residues: 49
  loop :  0.14 (0.58), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 436 
 HIS   0.002   0.001   HIS A   6 
 PHE   0.009   0.001   PHE B 464 
 TYR   0.010   0.001   TYR B 453 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00065 (    1)
  link_NAG-ASN         : angle       1.24345 (    3)
  link_BETA1-4         : bond        0.00297 (    1)
  link_BETA1-4         : angle       0.98167 (    3)
  hydrogen bonds       : bond        0.03649 (   93)
  hydrogen bonds       : angle       4.82048 (  240)
  link_BETA1-6         : bond        0.00689 (    1)
  link_BETA1-6         : angle       1.42261 (    3)
  SS BOND              : bond        0.00269 (    4)
  SS BOND              : angle       1.20439 (    8)
  covalent geometry    : bond        0.00359 ( 2082)
  covalent geometry    : angle       0.63209 ( 2830)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.8614 (mm) cc_final: 0.8259 (mt)
REVERT: A   34 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7515 (mp0)
REVERT: B  489 TYR cc_start: 0.7440 (m-80) cc_final: 0.6231 (m-80)
  outliers start: 7
  outliers final: 5
  residues processed: 36
  average time/residue: 0.1359
  time to fit residues: 5.8796
Evaluate side-chains
  38 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 6 optimal weight:    0.0570
   chunk 12 optimal weight:    0.1980
   chunk 5 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 23 optimal weight:    0.1980
   chunk 20 optimal weight:    0.0170
   chunk 15 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 14 optimal weight:    0.2980
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.1136

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.130588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.114056 restraints weight = 2936.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.116909 restraints weight = 1658.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.118809 restraints weight = 1140.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   2089  Z= 0.113
  Angle     :  0.658  13.024   2847  Z= 0.307
  Chirality :  0.047   0.395    318
  Planarity :  0.004   0.045    363
  Dihedral  :  5.635  55.019    344
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.43 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.54), residues: 254
  helix:  1.02 (0.58), residues: 88
  sheet: -0.13 (0.84), residues: 47
  loop :  0.14 (0.57), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 436 
 HIS   0.002   0.001   HIS A   6 
 PHE   0.008   0.001   PHE A  33 
 TYR   0.008   0.001   TYR A  14 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00049 (    1)
  link_NAG-ASN         : angle       1.11884 (    3)
  link_BETA1-4         : bond        0.00351 (    1)
  link_BETA1-4         : angle       0.98852 (    3)
  hydrogen bonds       : bond        0.03425 (   93)
  hydrogen bonds       : angle       4.78926 (  240)
  link_BETA1-6         : bond        0.00653 (    1)
  link_BETA1-6         : angle       1.28813 (    3)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       1.18074 (    8)
  covalent geometry    : bond        0.00249 ( 2082)
  covalent geometry    : angle       0.65380 ( 2830)

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

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

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  508 Ramachandran restraints generated.
    254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   25 ILE cc_start: 0.8610 (mm) cc_final: 0.8266 (mt)
REVERT: A   34 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7613 (mp0)
REVERT: B  489 TYR cc_start: 0.7384 (m-80) cc_final: 0.6239 (m-80)
  outliers start: 6
  outliers final: 5
  residues processed: 36
  average time/residue: 0.1319
  time to fit residues: 5.7302
Evaluate side-chains
  39 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 13 optimal weight:    0.2980
   chunk 8 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0020
   chunk 16 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0870
   overall best weight:    0.2966

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.127530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.110963 restraints weight = 2975.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.113826 restraints weight = 1680.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.115717 restraints weight = 1147.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.4271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2089  Z= 0.181
  Angle     :  0.693  13.098   2847  Z= 0.334
  Chirality :  0.048   0.375    318
  Planarity :  0.004   0.046    363
  Dihedral  :  5.671  52.842    344
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.93 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.54), residues: 254
  helix:  1.11 (0.59), residues: 88
  sheet: -0.31 (0.79), residues: 49
  loop :  0.09 (0.57), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 436 
 HIS   0.001   0.001   HIS A   6 
 PHE   0.009   0.001   PHE B 490 
 TYR   0.013   0.001   TYR B 453 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00154 (    1)
  link_NAG-ASN         : angle       1.40905 (    3)
  link_BETA1-4         : bond        0.00446 (    1)
  link_BETA1-4         : angle       1.00267 (    3)
  hydrogen bonds       : bond        0.03733 (   93)
  hydrogen bonds       : angle       5.06213 (  240)
  link_BETA1-6         : bond        0.00711 (    1)
  link_BETA1-6         : angle       1.56632 (    3)
  SS BOND              : bond        0.00225 (    4)
  SS BOND              : angle       1.23514 (    8)
  covalent geometry    : bond        0.00408 ( 2082)
  covalent geometry    : angle       0.68756 ( 2830)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1494.32 seconds
wall clock time: 26 minutes 32.71 seconds (1592.71 seconds total)