Starting phenix.real_space_refine
on Tue Mar  3 10:50:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zs5_11388/03_2026/6zs5_11388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zs5_11388/03_2026/6zs5_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zs5_11388/03_2026/6zs5_11388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zs5_11388/03_2026/6zs5_11388.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zs5_11388/03_2026/6zs5_11388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zs5_11388/03_2026/6zs5_11388.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 0.76, per 1000 atoms: 0.37
  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: 0.28
  Conformation dependent library (CDL) restraints added in 88.6 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: 0.11
  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: 0.30

  Time building geometry restraints manager: 0.33 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:             2.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.660
  Find NCS groups from input model:        0.010
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.150
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (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
 ARG   0.003   0.000   ARG A 395 
 TYR   0.027   0.003   TYR D 486 
 PHE   0.024   0.003   PHE A 423 
 TRP   0.013   0.003   TRP A 377 
 HIS   0.002   0.001   HIS D 565 

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

*********************** 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  : 0.094 
Fit side-chains
REVERT: A  375 ARG cc_start: 0.7475 (mtp180) cc_final: 0.6696 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1130
  time to fit residues: 7.8791
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  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.2980
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3503 r_free = 0.3503 target = 0.085189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.072173 restraints weight = 6021.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.074030 restraints weight = 3322.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.075316 restraints weight = 2209.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.076196 restraints weight = 1669.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.076788 restraints weight = 1377.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2081  Z= 0.161
  Angle     :  0.844  11.894   2823  Z= 0.389
  Chirality :  0.048   0.166    333
  Planarity :  0.005   0.047    352
  Dihedral  : 18.296 119.848    420
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.47), residues: 253
  helix:  None (None), residues: 0
  sheet: -0.44 (0.51), residues: 98
  loop : -2.33 (0.42), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 395 
 TYR   0.016   0.001   TYR D 486 
 PHE   0.011   0.001   PHE A 423 
 TRP   0.009   0.002   TRP A 377 
 HIS   0.001   0.000   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 2069)
  covalent geometry    : angle       0.73639 ( 2792)
  SS BOND              : bond        0.00130 (    5)
  SS BOND              : angle       1.06001 (   10)
  hydrogen bonds       : bond        0.04726 (   53)
  hydrogen bonds       : angle       6.72596 (  162)
  link_ALPHA1-3        : bond        0.01360 (    1)
  link_ALPHA1-3        : angle       2.50188 (    3)
  link_ALPHA1-6        : bond        0.01384 (    1)
  link_ALPHA1-6        : angle       1.81512 (    3)
  link_BETA1-4         : bond        0.01873 (    3)
  link_BETA1-4         : angle       4.80336 (    9)
  link_NAG-ASN         : bond        0.00347 (    2)
  link_NAG-ASN         : angle       6.43484 (    6)

*********************** 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  : 0.077 
Fit side-chains
REVERT: A  375 ARG cc_start: 0.7389 (mtp180) cc_final: 0.6606 (tpt170)
  outliers start: 9
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0770
  time to fit residues: 4.4735
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  : 0.093 
-------------------------------------------------------------------------------
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 10 optimal weight:    0.0870
   chunk 17 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0770
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.085990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.072695 restraints weight = 6141.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.074650 restraints weight = 3317.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.075994 restraints weight = 2180.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.076913 restraints weight = 1628.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.077515 restraints weight = 1333.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2967

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= 0.123
  Angle     :  0.757  11.404   2823  Z= 0.352
  Chirality :  0.048   0.201    333
  Planarity :  0.004   0.040    352
  Dihedral  : 14.666 116.062    420
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 22.79 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.48), residues: 253
  helix:  None (None), residues: 0
  sheet: -0.11 (0.50), residues: 98
  loop : -2.05 (0.44), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 395 
 TYR   0.009   0.001   TYR D 486 
 PHE   0.009   0.001   PHE A 423 
 TRP   0.007   0.002   TRP A 377 
 HIS   0.001   0.001   HIS D 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 2069)
  covalent geometry    : angle       0.65623 ( 2792)
  SS BOND              : bond        0.00066 (    5)
  SS BOND              : angle       0.60602 (   10)
  hydrogen bonds       : bond        0.03940 (   53)
  hydrogen bonds       : angle       5.88089 (  162)
  link_ALPHA1-3        : bond        0.01427 (    1)
  link_ALPHA1-3        : angle       2.95294 (    3)
  link_ALPHA1-6        : bond        0.01306 (    1)
  link_ALPHA1-6        : angle       1.49048 (    3)
  link_BETA1-4         : bond        0.01697 (    3)
  link_BETA1-4         : angle       4.67705 (    9)
  link_NAG-ASN         : bond        0.00342 (    2)
  link_NAG-ASN         : angle       5.51897 (    6)

*********************** 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
  51 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8278 (mtm110) cc_final: 0.7815 (mtm110)
REVERT: A  375 ARG cc_start: 0.7374 (mtp180) cc_final: 0.6676 (tpt170)
REVERT: A  420 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7657 (ptmt)
REVERT: D  576 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7863 (mp0)
  outliers start: 10
  outliers final: 5
  residues processed: 46
  average time/residue: 0.0844
  time to fit residues: 4.3916
Evaluate side-chains
  46 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 GLN
Chi-restraints excluded: chain A residue  382 THR
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0970
   chunk 18 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0670
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.4916

-------------------------------------------------------------------------------
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 = 0.3525 r_free = 0.3525 target = 0.086327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.073349 restraints weight = 6052.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.075304 restraints weight = 3203.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.076653 restraints weight = 2077.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.077577 restraints weight = 1538.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.078160 restraints weight = 1252.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2081  Z= 0.121
  Angle     :  0.734  10.801   2823  Z= 0.340
  Chirality :  0.048   0.216    333
  Planarity :  0.004   0.037    352
  Dihedral  : 14.116 115.464    420
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 21.40 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.48), residues: 253
  helix:  None (None), residues: 0
  sheet: -0.03 (0.50), residues: 98
  loop : -2.02 (0.43), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 395 
 TYR   0.007   0.001   TYR D 486 
 PHE   0.009   0.001   PHE A 423 
 TRP   0.007   0.001   TRP A 377 
 HIS   0.001   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 2069)
  covalent geometry    : angle       0.64175 ( 2792)
  SS BOND              : bond        0.00120 (    5)
  SS BOND              : angle       0.51354 (   10)
  hydrogen bonds       : bond        0.03476 (   53)
  hydrogen bonds       : angle       5.62753 (  162)
  link_ALPHA1-3        : bond        0.01382 (    1)
  link_ALPHA1-3        : angle       3.13049 (    3)
  link_ALPHA1-6        : bond        0.01173 (    1)
  link_ALPHA1-6        : angle       1.46022 (    3)
  link_BETA1-4         : bond        0.01614 (    3)
  link_BETA1-4         : angle       4.45735 (    9)
  link_NAG-ASN         : bond        0.00305 (    2)
  link_NAG-ASN         : angle       5.08171 (    6)

*********************** 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
  55 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8285 (mtm110) cc_final: 0.7839 (mtm110)
REVERT: A  375 ARG cc_start: 0.7350 (mtp180) cc_final: 0.6677 (tpt170)
REVERT: A  420 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7666 (ptmt)
REVERT: A  431 MET cc_start: 0.8814 (mmp) cc_final: 0.8552 (mmp)
REVERT: D  460 MET cc_start: 0.8162 (mtm) cc_final: 0.7833 (mtm)
REVERT: D  576 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8101 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 50
  average time/residue: 0.0783
  time to fit residues: 4.4419
Evaluate side-chains
  45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
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  525 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 13 optimal weight:    0.0020
   chunk 6 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.7188

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.086288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.073488 restraints weight = 6036.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.075427 restraints weight = 3234.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.076772 restraints weight = 2096.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.077698 restraints weight = 1552.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.078247 restraints weight = 1252.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2081  Z= 0.125
  Angle     :  0.725  10.399   2823  Z= 0.333
  Chirality :  0.048   0.223    333
  Planarity :  0.004   0.038    352
  Dihedral  : 13.355 114.870    420
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 20.93 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.48), residues: 253
  helix: -3.68 (1.34), residues: 6
  sheet:  0.19 (0.53), residues: 89
  loop : -2.09 (0.43), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 395 
 TYR   0.009   0.001   TYR D 486 
 PHE   0.010   0.001   PHE A 423 
 TRP   0.006   0.001   TRP A 377 
 HIS   0.001   0.000   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 2069)
  covalent geometry    : angle       0.64114 ( 2792)
  SS BOND              : bond        0.00199 (    5)
  SS BOND              : angle       0.49491 (   10)
  hydrogen bonds       : bond        0.03287 (   53)
  hydrogen bonds       : angle       5.42690 (  162)
  link_ALPHA1-3        : bond        0.01368 (    1)
  link_ALPHA1-3        : angle       3.12168 (    3)
  link_ALPHA1-6        : bond        0.01445 (    1)
  link_ALPHA1-6        : angle       1.44545 (    3)
  link_BETA1-4         : bond        0.01458 (    3)
  link_BETA1-4         : angle       4.30993 (    9)
  link_NAG-ASN         : bond        0.00214 (    2)
  link_NAG-ASN         : angle       4.69843 (    6)

*********************** 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
  52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7799 (mtm110)
REVERT: A  375 ARG cc_start: 0.7414 (mtp180) cc_final: 0.6730 (tpt170)
REVERT: D  576 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8129 (mp0)
  outliers start: 10
  outliers final: 7
  residues processed: 48
  average time/residue: 0.0827
  time to fit residues: 4.4759
Evaluate side-chains
  45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 GLN
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  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 20 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.084551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.071814 restraints weight = 5986.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.073730 restraints weight = 3225.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.075006 restraints weight = 2103.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.075858 restraints weight = 1576.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.076398 restraints weight = 1292.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2081  Z= 0.197
  Angle     :  0.765  10.583   2823  Z= 0.355
  Chirality :  0.048   0.221    333
  Planarity :  0.004   0.042    352
  Dihedral  : 13.122 115.547    420
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 22.79 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.49), residues: 253
  helix:  None (None), residues: 0
  sheet:  0.08 (0.53), residues: 90
  loop : -2.05 (0.44), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 459 
 TYR   0.021   0.002   TYR D 486 
 PHE   0.012   0.001   PHE A 423 
 TRP   0.009   0.002   TRP A 377 
 HIS   0.001   0.000   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 2069)
  covalent geometry    : angle       0.68481 ( 2792)
  SS BOND              : bond        0.00076 (    5)
  SS BOND              : angle       0.62704 (   10)
  hydrogen bonds       : bond        0.03661 (   53)
  hydrogen bonds       : angle       5.43954 (  162)
  link_ALPHA1-3        : bond        0.01392 (    1)
  link_ALPHA1-3        : angle       3.36016 (    3)
  link_ALPHA1-6        : bond        0.01255 (    1)
  link_ALPHA1-6        : angle       1.36889 (    3)
  link_BETA1-4         : bond        0.01328 (    3)
  link_BETA1-4         : angle       4.29981 (    9)
  link_NAG-ASN         : bond        0.00211 (    2)
  link_NAG-ASN         : angle       4.74471 (    6)

*********************** 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
  50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A  340 MET cc_start: 0.8776 (mmm) cc_final: 0.8519 (mtt)
REVERT: A  365 ARG cc_start: 0.8296 (mtm110) cc_final: 0.7874 (mtm110)
REVERT: A  375 ARG cc_start: 0.7334 (mtp180) cc_final: 0.6728 (tpt170)
REVERT: A  431 MET cc_start: 0.8852 (mmp) cc_final: 0.8592 (mmp)
REVERT: D  576 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8248 (mp0)
  outliers start: 11
  outliers final: 9
  residues processed: 45
  average time/residue: 0.0786
  time to fit residues: 4.0046
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  : 0.093 
-------------------------------------------------------------------------------
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  477 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  501 LEU
Chi-restraints excluded: chain D residue  503 MET
Chi-restraints excluded: chain D residue  509 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 4 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 14 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 = 0.3524 r_free = 0.3524 target = 0.086061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.072938 restraints weight = 6008.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.074971 restraints weight = 3099.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.076301 restraints weight = 2009.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.077145 restraints weight = 1500.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.077752 restraints weight = 1239.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2081  Z= 0.127
  Angle     :  0.725  10.027   2823  Z= 0.332
  Chirality :  0.046   0.232    333
  Planarity :  0.004   0.042    352
  Dihedral  : 12.410 113.558    420
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 21.86 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.49), residues: 253
  helix:  None (None), residues: 0
  sheet: -0.21 (0.50), residues: 99
  loop : -1.87 (0.46), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 395 
 TYR   0.012   0.001   TYR D 486 
 PHE   0.010   0.001   PHE A 423 
 TRP   0.006   0.001   TRP A 377 
 HIS   0.001   0.000   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2069)
  covalent geometry    : angle       0.64957 ( 2792)
  SS BOND              : bond        0.00064 (    5)
  SS BOND              : angle       0.46819 (   10)
  hydrogen bonds       : bond        0.03105 (   53)
  hydrogen bonds       : angle       5.04545 (  162)
  link_ALPHA1-3        : bond        0.01294 (    1)
  link_ALPHA1-3        : angle       3.30591 (    3)
  link_ALPHA1-6        : bond        0.01251 (    1)
  link_ALPHA1-6        : angle       1.36649 (    3)
  link_BETA1-4         : bond        0.01202 (    3)
  link_BETA1-4         : angle       4.11088 (    9)
  link_NAG-ASN         : bond        0.00219 (    2)
  link_NAG-ASN         : angle       4.35151 (    6)

*********************** 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
  53 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  340 MET cc_start: 0.8784 (mmm) cc_final: 0.8475 (mtt)
REVERT: A  365 ARG cc_start: 0.8255 (mtm110) cc_final: 0.7857 (mtm110)
REVERT: A  375 ARG cc_start: 0.7438 (mtp180) cc_final: 0.6810 (tpt170)
  outliers start: 14
  outliers final: 10
  residues processed: 47
  average time/residue: 0.0738
  time to fit residues: 3.9734
Evaluate side-chains
  50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 GLN
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  501 LEU
Chi-restraints excluded: chain D residue  503 MET
Chi-restraints excluded: chain D residue  504 THR
Chi-restraints excluded: chain D residue  509 THR
Chi-restraints excluded: chain D residue  525 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0980
   chunk 13 optimal weight:    0.0170
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7420

-------------------------------------------------------------------------------
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 = 0.085648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.072933 restraints weight = 6038.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.074886 restraints weight = 3163.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.076194 restraints weight = 2037.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.077060 restraints weight = 1513.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.077649 restraints weight = 1240.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3787

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     :  0.715   9.760   2823  Z= 0.327
  Chirality :  0.046   0.225    333
  Planarity :  0.003   0.041    352
  Dihedral  : 12.242 113.420    420
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 23.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.49), residues: 253
  helix:  None (None), residues: 0
  sheet:  0.03 (0.53), residues: 91
  loop : -1.93 (0.44), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 395 
 TYR   0.010   0.001   TYR D 486 
 PHE   0.009   0.001   PHE A 423 
 TRP   0.006   0.001   TRP A 377 
 HIS   0.001   0.000   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2069)
  covalent geometry    : angle       0.64211 ( 2792)
  SS BOND              : bond        0.00067 (    5)
  SS BOND              : angle       0.39629 (   10)
  hydrogen bonds       : bond        0.03051 (   53)
  hydrogen bonds       : angle       5.02452 (  162)
  link_ALPHA1-3        : bond        0.01308 (    1)
  link_ALPHA1-3        : angle       3.24928 (    3)
  link_ALPHA1-6        : bond        0.01258 (    1)
  link_ALPHA1-6        : angle       1.33455 (    3)
  link_BETA1-4         : bond        0.01149 (    3)
  link_BETA1-4         : angle       4.01189 (    9)
  link_NAG-ASN         : bond        0.00185 (    2)
  link_NAG-ASN         : angle       4.24785 (    6)

*********************** 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
  52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A  340 MET cc_start: 0.8752 (mmm) cc_final: 0.8479 (mtt)
REVERT: A  365 ARG cc_start: 0.8263 (mtm110) cc_final: 0.7840 (mtm110)
REVERT: A  375 ARG cc_start: 0.7412 (mtp180) cc_final: 0.6772 (tpt170)
REVERT: D  576 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8231 (mp0)
  outliers start: 12
  outliers final: 9
  residues processed: 46
  average time/residue: 0.0839
  time to fit residues: 4.3455
Evaluate side-chains
  49 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
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  503 MET
Chi-restraints excluded: chain D residue  504 THR
Chi-restraints excluded: chain D residue  509 THR
Chi-restraints excluded: chain D residue  525 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 18 optimal weight:    0.0170
   chunk 5 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5820

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.086347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.073704 restraints weight = 5945.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.075632 restraints weight = 3135.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.076933 restraints weight = 2029.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.077790 restraints weight = 1510.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.078310 restraints weight = 1238.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2081  Z= 0.115
  Angle     :  0.699   9.279   2823  Z= 0.322
  Chirality :  0.046   0.213    333
  Planarity :  0.003   0.040    352
  Dihedral  : 11.843 112.259    420
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 24.19 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.49), residues: 253
  helix:  None (None), residues: 0
  sheet:  0.10 (0.53), residues: 91
  loop : -1.91 (0.44), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 531 
 TYR   0.008   0.001   TYR D 486 
 PHE   0.009   0.001   PHE A 423 
 TRP   0.006   0.001   TRP A 377 
 HIS   0.001   0.000   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 2069)
  covalent geometry    : angle       0.63158 ( 2792)
  SS BOND              : bond        0.00077 (    5)
  SS BOND              : angle       0.35928 (   10)
  hydrogen bonds       : bond        0.03097 (   53)
  hydrogen bonds       : angle       5.11314 (  162)
  link_ALPHA1-3        : bond        0.01259 (    1)
  link_ALPHA1-3        : angle       3.14311 (    3)
  link_ALPHA1-6        : bond        0.01161 (    1)
  link_ALPHA1-6        : angle       1.30566 (    3)
  link_BETA1-4         : bond        0.01103 (    3)
  link_BETA1-4         : angle       3.81190 (    9)
  link_NAG-ASN         : bond        0.00189 (    2)
  link_NAG-ASN         : angle       4.05276 (    6)

*********************** 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
  49 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8243 (mtm110) cc_final: 0.7850 (mtm110)
REVERT: A  375 ARG cc_start: 0.7389 (mtp180) cc_final: 0.6783 (tpt170)
REVERT: D  576 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8232 (mp0)
  outliers start: 9
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0773
  time to fit residues: 4.0223
Evaluate side-chains
  47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
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  504 THR
Chi-restraints excluded: chain D residue  509 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0770
   chunk 3 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0470
   chunk 20 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.4236

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.087034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.074443 restraints weight = 6098.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.076410 restraints weight = 3167.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.077752 restraints weight = 2032.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.078612 restraints weight = 1498.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.079164 restraints weight = 1225.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.4159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2081  Z= 0.111
  Angle     :  0.732   8.890   2823  Z= 0.334
  Chirality :  0.046   0.198    333
  Planarity :  0.003   0.036    352
  Dihedral  : 11.553 111.260    420
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 24.19 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.50), residues: 253
  helix:  None (None), residues: 0
  sheet:  0.06 (0.53), residues: 91
  loop : -1.88 (0.45), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 459 
 TYR   0.006   0.001   TYR D 486 
 PHE   0.008   0.001   PHE A 423 
 TRP   0.005   0.001   TRP A 377 
 HIS   0.001   0.000   HIS D 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 2069)
  covalent geometry    : angle       0.67305 ( 2792)
  SS BOND              : bond        0.00067 (    5)
  SS BOND              : angle       0.37405 (   10)
  hydrogen bonds       : bond        0.02969 (   53)
  hydrogen bonds       : angle       5.27542 (  162)
  link_ALPHA1-3        : bond        0.01304 (    1)
  link_ALPHA1-3        : angle       3.11507 (    3)
  link_ALPHA1-6        : bond        0.01076 (    1)
  link_ALPHA1-6        : angle       1.30562 (    3)
  link_BETA1-4         : bond        0.01047 (    3)
  link_BETA1-4         : angle       3.66577 (    9)
  link_NAG-ASN         : bond        0.00210 (    2)
  link_NAG-ASN         : angle       3.91510 (    6)

********************** 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
  50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A  365 ARG cc_start: 0.8271 (mtm110) cc_final: 0.7880 (mtm110)
REVERT: A  375 ARG cc_start: 0.7502 (mtp180) cc_final: 0.6817 (tpt170)
REVERT: A  431 MET cc_start: 0.8832 (mmp) cc_final: 0.8537 (mmp)
REVERT: D  576 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8219 (mp0)
  outliers start: 9
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0668
  time to fit residues: 3.4587
Evaluate side-chains
  48 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0770
   chunk 21 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7340

-------------------------------------------------------------------------------
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 = 0.3534 r_free = 0.3534 target = 0.086294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.073749 restraints weight = 6178.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.075740 restraints weight = 3190.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.077087 restraints weight = 2038.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.077902 restraints weight = 1498.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.078478 restraints weight = 1233.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
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      :  0.003   0.028   2081  Z= 0.123
  Angle     :  0.720   8.762   2823  Z= 0.331
  Chirality :  0.046   0.185    333
  Planarity :  0.003   0.038    352
  Dihedral  : 11.325 109.954    420
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 25.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.50), residues: 253
  helix: -3.01 (1.80), residues: 6
  sheet:  0.06 (0.54), residues: 89
  loop : -2.10 (0.45), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 395 
 TYR   0.010   0.001   TYR D 486 
 PHE   0.008   0.001   PHE A 423 
 TRP   0.007   0.002   TRP A 377 
 HIS   0.001   0.000   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 2069)
  covalent geometry    : angle       0.66040 ( 2792)
  SS BOND              : bond        0.00061 (    5)
  SS BOND              : angle       0.49481 (   10)
  hydrogen bonds       : bond        0.03225 (   53)
  hydrogen bonds       : angle       5.15263 (  162)
  link_ALPHA1-3        : bond        0.01178 (    1)
  link_ALPHA1-3        : angle       3.04300 (    3)
  link_ALPHA1-6        : bond        0.01055 (    1)
  link_ALPHA1-6        : angle       1.28922 (    3)
  link_BETA1-4         : bond        0.00974 (    3)
  link_BETA1-4         : angle       3.58953 (    9)
  link_NAG-ASN         : bond        0.00130 (    2)
  link_NAG-ASN         : angle       3.93876 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 723.23 seconds
wall clock time: 12 minutes 55.40 seconds (775.40 seconds total)