Starting phenix.real_space_refine
on Wed Jul 23 07:57:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zs5_11388/07_2025/6zs5_11388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zs5_11388/07_2025/6zs5_11388.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/6zs5_11388/07_2025/6zs5_11388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zs5_11388/07_2025/6zs5_11388.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zs5_11388/07_2025/6zs5_11388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zs5_11388/07_2025/6zs5_11388.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=   0.001 sd=   0.082
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      21      5.16       5
     C    1261      2.51       5
     N     341      2.21       5
     O     413      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 2036
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 911
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
    Chain: "D"
      Number of atoms: 1036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1036
          Classifications: {'peptide': 141}
          Incomplete info: {'backbone_only': 12}
          Link IDs: {'PTRANS': 6, 'TRANS': 134}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 89
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.31, per 1000 atoms: 1.13
  Number of scatterers: 2036
  At special positions: 0
  Unit cell: (72.628, 71.544, 88.888, 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      21     16.00
     O     413      8.00
     N     341      7.00
     C    1261      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 335 " - pdb=" SG  CYS A 425 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 366 " - pdb=" SG  CYS A 389 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 506 " - pdb=" SG  CYS D 566 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 527 " - pdb=" SG  CYS D 582 " distance=1.59
    Simple disulfide: pdb=" SG  CYS D 571 " - pdb=" SG  CYS D 578 " distance=1.89

  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
    ALPHA1-3
      " BMA B   3 " - " MAN B   4 "
    ALPHA1-6
      " BMA B   3 " - " MAN B   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 396 "
      " NAG C   1 " - " ASN D 513 "
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 251.4 milliseconds
  

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  456

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 43.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 333
      removed outlier: 3.661A  pdb=" N   VAL A 342 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360
      removed outlier: 3.662A  pdb=" N   ASN A 404 " --> pdb=" O   PHE A 423 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ILE A 419 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 395
      removed outlier: 3.662A  pdb=" N   ASN A 404 " --> pdb=" O   PHE A 423 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ILE A 419 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434
      removed outlier: 6.680A  pdb=" N   TYR D 563 " --> pdb=" O   ALA D 508 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ALA D 508 " --> pdb=" O   TYR D 563 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   HIS D 565 " --> pdb=" O   CYS D 506 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   CYS D 506 " --> pdb=" O   HIS D 565 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLU D 567 " --> pdb=" O   THR D 504 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   CYS D 506 " --> pdb=" O   ILE D 522 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 438 through 440
      removed outlier: 6.863A  pdb=" N   ALA A 438 " --> pdb=" O   VAL D 477 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'D' and resid 458 through 463
      removed outlier: 4.017A  pdb=" N   TYR D 486 " --> pdb=" O   PHE D 463 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL D 550 " --> pdb=" O   LEU D 485 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   ARG D 547 " --> pdb=" O   VAL D 538 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL D 538 " --> pdb=" O   ARG D 547 " (cutoff:3.500A)

    61 hydrogen bonds defined for protein.
    162 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: 0.46

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 332
        1.31 -     1.44: 558
        1.44 -     1.57: 1145
        1.57 -     1.70: 3
        1.70 -     1.83: 31
  Bond restraints: 2069
  Sorted by residual:
  bond pdb=" CA  SER D 583 "
       pdb=" C   SER D 583 "
    ideal  model  delta    sigma   weight residual
    1.520  1.462  0.059 1.20e-02 6.94e+03 2.41e+01
  bond pdb=" C   SER D 583 "
       pdb=" O   SER D 583 "
    ideal  model  delta    sigma   weight residual
    1.234  1.180  0.055 1.15e-02 7.56e+03 2.28e+01
  bond pdb=" CA  THR D 581 "
       pdb=" C   THR D 581 "
    ideal  model  delta    sigma   weight residual
    1.523  1.484  0.039 1.21e-02 6.83e+03 1.06e+01
  bond pdb=" CA  SER D 583 "
       pdb=" CB  SER D 583 "
    ideal  model  delta    sigma   weight residual
    1.533  1.479  0.054 1.69e-02 3.50e+03 1.02e+01
  bond pdb=" N   THR D 581 "
       pdb=" CA  THR D 581 "
    ideal  model  delta    sigma   weight residual
    1.460  1.423  0.036 1.20e-02 6.94e+03 9.24e+00
  ... (remaining 2064 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 2659
        2.18 -     4.37: 101
        4.37 -     6.55: 28
        6.55 -     8.74: 3
        8.74 -    10.92: 1
  Bond angle restraints: 2792
  Sorted by residual:
  angle pdb=" C   LYS D 579 "
        pdb=" N   PRO D 580 "
        pdb=" CA  PRO D 580 "
      ideal   model   delta    sigma   weight residual
     119.76  125.33   -5.57 1.03e+00 9.43e-01 2.92e+01
  angle pdb=" N   GLY A 387 "
        pdb=" CA  GLY A 387 "
        pdb=" C   GLY A 387 "
      ideal   model   delta    sigma   weight residual
     112.34  123.26  -10.92 2.04e+00 2.40e-01 2.87e+01
  angle pdb=" N   THR D 581 "
        pdb=" CA  THR D 581 "
        pdb=" C   THR D 581 "
      ideal   model   delta    sigma   weight residual
     108.02  100.12    7.90 1.75e+00 3.27e-01 2.04e+01
  angle pdb=" C   THR D 581 "
        pdb=" CA  THR D 581 "
        pdb=" CB  THR D 581 "
      ideal   model   delta    sigma   weight residual
     110.74  104.22    6.52 1.61e+00 3.86e-01 1.64e+01
  angle pdb=" CA  PRO D 580 "
        pdb=" C   PRO D 580 "
        pdb=" N   THR D 581 "
      ideal   model   delta    sigma   weight residual
     115.56  110.66    4.90 1.27e+00 6.20e-01 1.49e+01
  ... (remaining 2787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.21: 1238
       24.21 -    48.41: 63
       48.41 -    72.62: 6
       72.62 -    96.82: 18
       96.82 -   121.02: 9
  Dihedral angle restraints: 1334
    sinusoidal: 613
      harmonic: 721
  Sorted by residual:
  dihedral pdb=" CA  LYS A 346 "
           pdb=" C   LYS A 346 "
           pdb=" N   CYS A 347 "
           pdb=" CA  CYS A 347 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.31   29.69     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" N   THR D 581 "
           pdb=" C   THR D 581 "
           pdb=" CA  THR D 581 "
           pdb=" CB  THR D 581 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  109.35   14.05     0      2.50e+00 1.60e-01 3.16e+01
  dihedral pdb=" C   THR D 581 "
           pdb=" N   THR D 581 "
           pdb=" CA  THR D 581 "
           pdb=" CB  THR D 581 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -108.06  -13.94     0      2.50e+00 1.60e-01 3.11e+01
  ... (remaining 1331 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 256
       0.068 -    0.137: 68
       0.137 -    0.205: 4
       0.205 -    0.273: 3
       0.273 -    0.342: 2
  Chirality restraints: 333
  Sorted by residual:
  chirality pdb=" CA  THR D 581 "
            pdb=" N   THR D 581 "
            pdb=" C   THR D 581 "
            pdb=" CB  THR D 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.87   -0.34 2.00e-01 2.50e+01 2.92e+00
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.62    0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" C2  BMA B   3 "
            pdb=" C1  BMA B   3 "
            pdb=" C3  BMA B   3 "
            pdb=" O2  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.74   -0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 330 not shown)

  Planarity restraints: 354
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D 525 "   -0.015 2.00e-02 2.50e+03   3.05e-02 9.30e+00
        pdb=" CG  ASP D 525 "    0.053 2.00e-02 2.50e+03
        pdb=" OD1 ASP D 525 "   -0.019 2.00e-02 2.50e+03
        pdb=" OD2 ASP D 525 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 386 "   -0.012 2.00e-02 2.50e+03   2.46e-02 6.04e+00
        pdb=" CG  ASP A 386 "    0.042 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 386 "   -0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 386 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 387 "   -0.041 5.00e-02 4.00e+02   6.06e-02 5.87e+00
        pdb=" N   PRO A 388 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 388 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 388 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 351 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 186
        2.74 -     3.28: 1655
        3.28 -     3.82: 2977
        3.82 -     4.36: 3207
        4.36 -     4.90: 5904
  Nonbonded interactions: 13929
  Sorted by model distance:
  nonbonded pdb=" O   THR D 581 "
            pdb=" OG1 THR D 581 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OD1 ASP D 532 "
            pdb=" OG1 THR D 534 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG  SER A 362 "
            pdb=" OD1 ASN A 404 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OG  SER D 543 "
            pdb=" N   SER D 544 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" OH  TYR A 402 "
            pdb=" OD2 ASP D 495 "
     model   vdw
     2.369 3.040
  ... (remaining 13924 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:             1.340
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     10.710
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
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      :  0.013   0.438   2081  Z= 0.660
  Angle     :  1.367  22.944   2823  Z= 0.691
  Chirality :  0.067   0.342    333
  Planarity :  0.008   0.061    352
  Dihedral  : 21.400 121.023    863
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Cbeta Deviations :  0.44 %
  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: -2.98 (0.45), residues: 253
  helix:  None (None), residues: 0
  sheet: -1.19 (0.53), residues: 92
  loop : -2.61 (0.37), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP A 377 
 HIS   0.002   0.001   HIS D 565 
 PHE   0.024   0.003   PHE A 423 
 TYR   0.027   0.003   TYR D 486 
 ARG   0.003   0.000   ARG A 395 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00391 (    2)
  link_NAG-ASN         : angle       8.07290 (    6)
  link_ALPHA1-6        : bond        0.01075 (    1)
  link_ALPHA1-6        : angle       1.86495 (    3)
  link_BETA1-4         : bond        0.02124 (    3)
  link_BETA1-4         : angle       6.23863 (    9)
  link_ALPHA1-3        : bond        0.00788 (    1)
  link_ALPHA1-3        : angle       1.61819 (    3)
  hydrogen bonds       : bond        0.28007 (   53)
  hydrogen bonds       : angle      10.55124 (  162)
  SS BOND              : bond        0.20505 (    5)
  SS BOND              : angle      11.03486 (   10)
  covalent geometry    : bond        0.00847 ( 2069)
  covalent geometry    : angle       1.08744 ( 2792)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  375 ARG cc_start: 0.7475 (mtp180) cc_final: 0.6656 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.2361
  time to fit residues: 16.5136
Evaluate side-chains
  45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 348 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.085400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.072372 restraints weight = 6062.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.074231 restraints weight = 3324.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.075521 restraints weight = 2206.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2081  Z= 0.156
  Angle     :  0.836  12.014   2823  Z= 0.385
  Chirality :  0.047   0.173    333
  Planarity :  0.005   0.046    352
  Dihedral  : 18.044 119.795    420
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 23.26 %
    Favored  : 72.56 %
  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: -2.25 (0.47), residues: 253
  helix:  None (None), residues: 0
  sheet: -0.44 (0.50), residues: 98
  loop : -2.33 (0.41), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 377 
 HIS   0.001   0.001   HIS A 331 
 PHE   0.011   0.001   PHE D 548 
 TYR   0.014   0.001   TYR D 486 
 ARG   0.004   0.001   ARG A 395 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00275 (    2)
  link_NAG-ASN         : angle       6.37140 (    6)
  link_ALPHA1-6        : bond        0.01300 (    1)
  link_ALPHA1-6        : angle       1.81988 (    3)
  link_BETA1-4         : bond        0.02047 (    3)
  link_BETA1-4         : angle       4.80275 (    9)
  link_ALPHA1-3        : bond        0.01288 (    1)
  link_ALPHA1-3        : angle       2.47812 (    3)
  hydrogen bonds       : bond        0.04537 (   53)
  hydrogen bonds       : angle       6.64945 (  162)
  SS BOND              : bond        0.00114 (    5)
  SS BOND              : angle       0.93647 (   10)
  covalent geometry    : bond        0.00319 ( 2069)
  covalent geometry    : angle       0.72901 ( 2792)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  375 ARG cc_start: 0.7368 (mtp180) cc_final: 0.6518 (tpt170)
  outliers start: 9
  outliers final: 4
  residues processed: 51
  average time/residue: 0.1674
  time to fit residues: 9.7437
Evaluate side-chains
  45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  501 LEU
Chi-restraints excluded: chain D residue  525 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0170
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.1624

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

Flipped N/Q/H residues before XYZ refinement:
A 348 GLN
D 524 GLN
D 565 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.084631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.071533 restraints weight = 6065.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.073375 restraints weight = 3318.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.074646 restraints weight = 2199.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2081  Z= 0.153
  Angle     :  0.772  11.458   2823  Z= 0.362
  Chirality :  0.048   0.208    333
  Planarity :  0.004   0.044    352
  Dihedral  : 14.463 116.222    420
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 21.86 %
    Favored  : 72.09 %
  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: -1.90 (0.48), residues: 253
  helix:  None (None), residues: 0
  sheet: -0.12 (0.50), residues: 96
  loop : -2.14 (0.43), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 377 
 HIS   0.001   0.001   HIS D 529 
 PHE   0.011   0.001   PHE A 423 
 TYR   0.016   0.001   TYR D 486 
 ARG   0.003   0.000   ARG A 395 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00227 (    2)
  link_NAG-ASN         : angle       5.51323 (    6)
  link_ALPHA1-6        : bond        0.01323 (    1)
  link_ALPHA1-6        : angle       1.47188 (    3)
  link_BETA1-4         : bond        0.01615 (    3)
  link_BETA1-4         : angle       4.66819 (    9)
  link_ALPHA1-3        : bond        0.01322 (    1)
  link_ALPHA1-3        : angle       3.07424 (    3)
  hydrogen bonds       : bond        0.04107 (   53)
  hydrogen bonds       : angle       5.92713 (  162)
  SS BOND              : bond        0.00125 (    5)
  SS BOND              : angle       0.75696 (   10)
  covalent geometry    : bond        0.00333 ( 2069)
  covalent geometry    : angle       0.67266 ( 2792)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8337 (mtm110) cc_final: 0.7868 (mtm110)
REVERT: A  375 ARG cc_start: 0.7414 (mtp180) cc_final: 0.6665 (tpt170)
REVERT: A  420 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7702 (ptmt)
REVERT: D  576 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7879 (mp0)
  outliers start: 13
  outliers final: 8
  residues processed: 45
  average time/residue: 0.1908
  time to fit residues: 9.8208
Evaluate side-chains
  46 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  501 LEU
Chi-restraints excluded: chain D residue  509 THR
Chi-restraints excluded: chain D residue  525 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 348 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.085272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.072543 restraints weight = 5866.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.074412 restraints weight = 3153.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.075690 restraints weight = 2067.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2081  Z= 0.136
  Angle     :  0.747  10.906   2823  Z= 0.349
  Chirality :  0.048   0.223    333
  Planarity :  0.004   0.042    352
  Dihedral  : 14.040 115.664    420
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 20.93 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.48), residues: 253
  helix:  None (None), residues: 0
  sheet: -0.08 (0.50), residues: 98
  loop : -2.05 (0.44), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 377 
 HIS   0.003   0.001   HIS D 565 
 PHE   0.009   0.001   PHE A 423 
 TYR   0.012   0.001   TYR D 486 
 ARG   0.002   0.000   ARG D 531 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00235 (    2)
  link_NAG-ASN         : angle       5.10344 (    6)
  link_ALPHA1-6        : bond        0.01351 (    1)
  link_ALPHA1-6        : angle       1.47296 (    3)
  link_BETA1-4         : bond        0.01487 (    3)
  link_BETA1-4         : angle       4.46890 (    9)
  link_ALPHA1-3        : bond        0.01304 (    1)
  link_ALPHA1-3        : angle       3.17050 (    3)
  hydrogen bonds       : bond        0.03639 (   53)
  hydrogen bonds       : angle       5.71833 (  162)
  SS BOND              : bond        0.00094 (    5)
  SS BOND              : angle       0.55214 (   10)
  covalent geometry    : bond        0.00298 ( 2069)
  covalent geometry    : angle       0.65521 ( 2792)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8301 (mtm110) cc_final: 0.7856 (mtm110)
REVERT: A  375 ARG cc_start: 0.7374 (mtp180) cc_final: 0.6653 (tpt170)
REVERT: A  420 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7715 (ptmt)
REVERT: A  431 MET cc_start: 0.8868 (mmp) cc_final: 0.8601 (mmp)
REVERT: D  460 MET cc_start: 0.8206 (mtm) cc_final: 0.7849 (mtm)
REVERT: D  524 GLN cc_start: 0.8504 (tp-100) cc_final: 0.8260 (tp40)
REVERT: D  567 GLU cc_start: 0.7856 (pt0) cc_final: 0.7613 (pt0)
REVERT: D  576 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8110 (mp0)
  outliers start: 12
  outliers final: 7
  residues processed: 48
  average time/residue: 0.1711
  time to fit residues: 9.3511
Evaluate side-chains
  47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  501 LEU
Chi-restraints excluded: chain D residue  509 THR
Chi-restraints excluded: chain D residue  560 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 348 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.085623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.072875 restraints weight = 6084.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.074781 restraints weight = 3168.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.076087 restraints weight = 2060.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2081  Z= 0.132
  Angle     :  0.739  10.589   2823  Z= 0.339
  Chirality :  0.047   0.230    333
  Planarity :  0.004   0.042    352
  Dihedral  : 13.320 114.877    420
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 20.47 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.49), residues: 253
  helix:  None (None), residues: 0
  sheet:  0.04 (0.51), residues: 98
  loop : -1.99 (0.45), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 377 
 HIS   0.002   0.001   HIS D 565 
 PHE   0.010   0.001   PHE A 423 
 TYR   0.011   0.001   TYR D 486 
 ARG   0.002   0.000   ARG A 395 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00216 (    2)
  link_NAG-ASN         : angle       4.70045 (    6)
  link_ALPHA1-6        : bond        0.01355 (    1)
  link_ALPHA1-6        : angle       1.40790 (    3)
  link_BETA1-4         : bond        0.01378 (    3)
  link_BETA1-4         : angle       4.36498 (    9)
  link_ALPHA1-3        : bond        0.01325 (    1)
  link_ALPHA1-3        : angle       3.14382 (    3)
  hydrogen bonds       : bond        0.03343 (   53)
  hydrogen bonds       : angle       5.52028 (  162)
  SS BOND              : bond        0.00077 (    5)
  SS BOND              : angle       0.50079 (   10)
  covalent geometry    : bond        0.00293 ( 2069)
  covalent geometry    : angle       0.65507 ( 2792)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8350 (mtm110) cc_final: 0.7910 (mtm110)
REVERT: A  375 ARG cc_start: 0.7301 (mtp180) cc_final: 0.6635 (tpt170)
REVERT: A  420 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7663 (ptmt)
REVERT: A  431 MET cc_start: 0.8886 (mmp) cc_final: 0.8677 (mmp)
REVERT: D  576 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8081 (mp0)
  outliers start: 12
  outliers final: 9
  residues processed: 49
  average time/residue: 0.1717
  time to fit residues: 9.6079
Evaluate side-chains
  49 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  420 LYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  501 LEU
Chi-restraints excluded: chain D residue  509 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.3499 r_free = 0.3499 target = 0.084686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.071556 restraints weight = 5994.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.073502 restraints weight = 3159.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.074790 restraints weight = 2056.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2081  Z= 0.197
  Angle     :  0.771  10.591   2823  Z= 0.363
  Chirality :  0.047   0.228    333
  Planarity :  0.004   0.046    352
  Dihedral  : 12.956 115.145    420
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  7.44 %
    Allowed  : 20.93 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.49), residues: 253
  helix:  None (None), residues: 0
  sheet:  0.14 (0.54), residues: 91
  loop : -2.06 (0.43), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 377 
 HIS   0.003   0.001   HIS D 565 
 PHE   0.012   0.001   PHE A 423 
 TYR   0.024   0.002   TYR D 486 
 ARG   0.003   0.000   ARG D 459 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00278 (    2)
  link_NAG-ASN         : angle       4.71789 (    6)
  link_ALPHA1-6        : bond        0.01381 (    1)
  link_ALPHA1-6        : angle       1.33699 (    3)
  link_BETA1-4         : bond        0.01189 (    3)
  link_BETA1-4         : angle       4.31097 (    9)
  link_ALPHA1-3        : bond        0.01153 (    1)
  link_ALPHA1-3        : angle       3.23478 (    3)
  hydrogen bonds       : bond        0.03892 (   53)
  hydrogen bonds       : angle       5.56946 (  162)
  SS BOND              : bond        0.00123 (    5)
  SS BOND              : angle       0.65132 (   10)
  covalent geometry    : bond        0.00445 ( 2069)
  covalent geometry    : angle       0.69189 ( 2792)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  340 MET cc_start: 0.8785 (mmm) cc_final: 0.8548 (mtt)
REVERT: A  365 ARG cc_start: 0.8315 (mtm110) cc_final: 0.7900 (mtm110)
REVERT: A  375 ARG cc_start: 0.7429 (mtp180) cc_final: 0.6758 (tpt170)
REVERT: A  431 MET cc_start: 0.8925 (mmp) cc_final: 0.8671 (mmp)
  outliers start: 16
  outliers final: 10
  residues processed: 49
  average time/residue: 0.1681
  time to fit residues: 9.4042
Evaluate side-chains
  49 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  504 THR
Chi-restraints excluded: chain D residue  509 THR
Chi-restraints excluded: chain D residue  560 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.3495 r_free = 0.3495 target = 0.084737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.072079 restraints weight = 6138.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.074053 restraints weight = 3158.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.075368 restraints weight = 2008.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2081  Z= 0.135
  Angle     :  0.717  10.165   2823  Z= 0.332
  Chirality :  0.046   0.233    333
  Planarity :  0.004   0.042    352
  Dihedral  : 12.409 113.573    420
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 23.26 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.49), residues: 253
  helix:  None (None), residues: 0
  sheet:  0.20 (0.54), residues: 91
  loop : -2.05 (0.43), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 377 
 HIS   0.002   0.001   HIS D 565 
 PHE   0.009   0.001   PHE A 423 
 TYR   0.012   0.001   TYR D 486 
 ARG   0.001   0.000   ARG A 395 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    2)
  link_NAG-ASN         : angle       4.38559 (    6)
  link_ALPHA1-6        : bond        0.01229 (    1)
  link_ALPHA1-6        : angle       1.34218 (    3)
  link_BETA1-4         : bond        0.01173 (    3)
  link_BETA1-4         : angle       4.14745 (    9)
  link_ALPHA1-3        : bond        0.01269 (    1)
  link_ALPHA1-3        : angle       3.33250 (    3)
  hydrogen bonds       : bond        0.03400 (   53)
  hydrogen bonds       : angle       5.33719 (  162)
  SS BOND              : bond        0.00062 (    5)
  SS BOND              : angle       0.49262 (   10)
  covalent geometry    : bond        0.00303 ( 2069)
  covalent geometry    : angle       0.63898 ( 2792)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  340 MET cc_start: 0.8771 (mmm) cc_final: 0.8485 (mtt)
REVERT: A  365 ARG cc_start: 0.8319 (mtm110) cc_final: 0.7900 (mtm110)
REVERT: A  375 ARG cc_start: 0.7440 (mtp180) cc_final: 0.6733 (tpt170)
REVERT: A  431 MET cc_start: 0.8898 (mmp) cc_final: 0.8625 (mmp)
REVERT: D  503 MET cc_start: 0.7708 (mtt) cc_final: 0.7473 (mtm)
REVERT: D  576 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8182 (mp0)
  outliers start: 12
  outliers final: 9
  residues processed: 47
  average time/residue: 0.1610
  time to fit residues: 8.6766
Evaluate side-chains
  47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  504 THR
Chi-restraints excluded: chain D residue  509 THR
Chi-restraints excluded: chain D residue  560 ASP
Chi-restraints excluded: chain D residue  567 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 18 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3525 r_free = 0.3525 target = 0.086106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.072984 restraints weight = 6044.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.074997 restraints weight = 3145.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.076344 restraints weight = 2043.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2081  Z= 0.126
  Angle     :  0.718   9.755   2823  Z= 0.332
  Chirality :  0.046   0.222    333
  Planarity :  0.003   0.041    352
  Dihedral  : 12.104 113.048    420
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 24.19 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.49), residues: 253
  helix:  None (None), residues: 0
  sheet: -0.06 (0.51), residues: 99
  loop : -2.00 (0.45), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 377 
 HIS   0.002   0.001   HIS D 565 
 PHE   0.009   0.001   PHE A 423 
 TYR   0.010   0.001   TYR D 486 
 ARG   0.001   0.000   ARG A 395 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00184 (    2)
  link_NAG-ASN         : angle       4.23826 (    6)
  link_ALPHA1-6        : bond        0.01245 (    1)
  link_ALPHA1-6        : angle       1.30906 (    3)
  link_BETA1-4         : bond        0.01144 (    3)
  link_BETA1-4         : angle       3.98809 (    9)
  link_ALPHA1-3        : bond        0.01270 (    1)
  link_ALPHA1-3        : angle       3.24198 (    3)
  hydrogen bonds       : bond        0.03232 (   53)
  hydrogen bonds       : angle       5.19432 (  162)
  SS BOND              : bond        0.00070 (    5)
  SS BOND              : angle       0.43305 (   10)
  covalent geometry    : bond        0.00279 ( 2069)
  covalent geometry    : angle       0.64579 ( 2792)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  340 MET cc_start: 0.8716 (mmm) cc_final: 0.8473 (mtt)
REVERT: A  365 ARG cc_start: 0.8279 (mtm110) cc_final: 0.7880 (mtm110)
REVERT: A  375 ARG cc_start: 0.7423 (mtp180) cc_final: 0.6748 (tpt170)
REVERT: D  576 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8180 (mp0)
  outliers start: 11
  outliers final: 9
  residues processed: 45
  average time/residue: 0.1649
  time to fit residues: 8.4798
Evaluate side-chains
  47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  504 THR
Chi-restraints excluded: chain D residue  509 THR
Chi-restraints excluded: chain D residue  525 ASP
Chi-restraints excluded: chain D residue  560 ASP
Chi-restraints excluded: chain D residue  567 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.6560

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.085756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.073054 restraints weight = 6157.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.075004 restraints weight = 3150.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.076312 restraints weight = 2017.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2081  Z= 0.115
  Angle     :  0.706   9.246   2823  Z= 0.324
  Chirality :  0.045   0.206    333
  Planarity :  0.003   0.040    352
  Dihedral  : 11.649 111.554    420
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 24.65 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.49), residues: 253
  helix: -3.39 (1.35), residues: 6
  sheet: -0.04 (0.51), residues: 98
  loop : -2.15 (0.45), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 377 
 HIS   0.002   0.001   HIS D 565 
 PHE   0.008   0.001   PHE A 423 
 TYR   0.008   0.001   TYR D 486 
 ARG   0.001   0.000   ARG D 459 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00184 (    2)
  link_NAG-ASN         : angle       4.02171 (    6)
  link_ALPHA1-6        : bond        0.01110 (    1)
  link_ALPHA1-6        : angle       1.29376 (    3)
  link_BETA1-4         : bond        0.01059 (    3)
  link_BETA1-4         : angle       3.77409 (    9)
  link_ALPHA1-3        : bond        0.01247 (    1)
  link_ALPHA1-3        : angle       3.13882 (    3)
  hydrogen bonds       : bond        0.02983 (   53)
  hydrogen bonds       : angle       5.15917 (  162)
  SS BOND              : bond        0.00075 (    5)
  SS BOND              : angle       0.37045 (   10)
  covalent geometry    : bond        0.00253 ( 2069)
  covalent geometry    : angle       0.64053 ( 2792)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7936 (mtm110)
REVERT: A  375 ARG cc_start: 0.7534 (mtp180) cc_final: 0.6753 (tpt170)
REVERT: A  431 MET cc_start: 0.8899 (mmp) cc_final: 0.8615 (mmp)
REVERT: D  576 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8169 (mp0)
  outliers start: 11
  outliers final: 9
  residues processed: 47
  average time/residue: 0.1799
  time to fit residues: 9.6600
Evaluate side-chains
  48 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  504 THR
Chi-restraints excluded: chain D residue  509 THR
Chi-restraints excluded: chain D residue  525 ASP
Chi-restraints excluded: chain D residue  560 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0980
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.086521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.073382 restraints weight = 6033.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.075370 restraints weight = 3099.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.076698 restraints weight = 2015.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2081  Z= 0.126
  Angle     :  0.725   9.026   2823  Z= 0.334
  Chirality :  0.045   0.193    333
  Planarity :  0.003   0.040    352
  Dihedral  : 11.427 110.465    420
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 25.58 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.49), residues: 253
  helix: -3.27 (1.58), residues: 6
  sheet:  0.17 (0.54), residues: 90
  loop : -2.19 (0.44), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 377 
 HIS   0.003   0.001   HIS D 565 
 PHE   0.008   0.001   PHE A 423 
 TYR   0.011   0.001   TYR D 486 
 ARG   0.001   0.000   ARG A 395 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00146 (    2)
  link_NAG-ASN         : angle       3.99587 (    6)
  link_ALPHA1-6        : bond        0.01054 (    1)
  link_ALPHA1-6        : angle       1.27407 (    3)
  link_BETA1-4         : bond        0.00983 (    3)
  link_BETA1-4         : angle       3.68263 (    9)
  link_ALPHA1-3        : bond        0.01180 (    1)
  link_ALPHA1-3        : angle       3.08187 (    3)
  hydrogen bonds       : bond        0.03029 (   53)
  hydrogen bonds       : angle       5.30720 (  162)
  SS BOND              : bond        0.00046 (    5)
  SS BOND              : angle       0.33163 (   10)
  covalent geometry    : bond        0.00288 ( 2069)
  covalent geometry    : angle       0.66376 ( 2792)

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

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

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  506 Ramachandran restraints generated.
    253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8260 (mtm110) cc_final: 0.7894 (mtm110)
REVERT: A  375 ARG cc_start: 0.7540 (mtp180) cc_final: 0.6784 (tpt170)
REVERT: A  431 MET cc_start: 0.8925 (mmp) cc_final: 0.8644 (mmp)
REVERT: D  576 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8182 (mp0)
  outliers start: 9
  outliers final: 9
  residues processed: 45
  average time/residue: 0.1869
  time to fit residues: 9.6102
Evaluate side-chains
  48 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain D residue  477 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  504 THR
Chi-restraints excluded: chain D residue  509 THR
Chi-restraints excluded: chain D residue  525 ASP
Chi-restraints excluded: chain D residue  560 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 19 optimal weight:    0.2980
   chunk 18 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.086869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.073633 restraints weight = 5963.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.075664 restraints weight = 3072.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.077026 restraints weight = 1976.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2081  Z= 0.120
  Angle     :  0.709   8.807   2823  Z= 0.327
  Chirality :  0.044   0.177    333
  Planarity :  0.003   0.040    352
  Dihedral  : 11.089 108.209    420
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 26.05 %
    Favored  : 68.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.50), residues: 253
  helix: -3.08 (1.75), residues: 6
  sheet:  0.28 (0.55), residues: 90
  loop : -2.14 (0.44), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 377 
 HIS   0.002   0.001   HIS D 565 
 PHE   0.007   0.001   PHE A 423 
 TYR   0.009   0.001   TYR D 486 
 ARG   0.001   0.000   ARG A 395 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00160 (    2)
  link_NAG-ASN         : angle       3.91897 (    6)
  link_ALPHA1-6        : bond        0.00953 (    1)
  link_ALPHA1-6        : angle       1.29548 (    3)
  link_BETA1-4         : bond        0.00983 (    3)
  link_BETA1-4         : angle       3.57213 (    9)
  link_ALPHA1-3        : bond        0.01213 (    1)
  link_ALPHA1-3        : angle       3.07549 (    3)
  hydrogen bonds       : bond        0.02989 (   53)
  hydrogen bonds       : angle       5.15329 (  162)
  SS BOND              : bond        0.00043 (    5)
  SS BOND              : angle       0.34921 (   10)
  covalent geometry    : bond        0.00270 ( 2069)
  covalent geometry    : angle       0.64942 ( 2792)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1299.38 seconds
wall clock time: 22 minutes 59.72 seconds (1379.72 seconds total)