Starting phenix.real_space_refine
on Tue Mar  3 15:27:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x8y_33060/03_2026/7x8y_33060_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x8y_33060/03_2026/7x8y_33060.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x8y_33060/03_2026/7x8y_33060.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x8y_33060/03_2026/7x8y_33060.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x8y_33060/03_2026/7x8y_33060_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x8y_33060/03_2026/7x8y_33060_trim.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2183      2.51       5
     N     575      2.21       5
     O     662      1.98       5
     H    3296      0.53       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: 6731
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3222
          Classifications: {'peptide': 208}
          Link IDs: {'PTRANS': 12, 'TRANS': 195}
    Chain: "H"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 1865
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 5, 'TRANS': 119}
    Chain: "L"
      Number of atoms: 1630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 1630
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.50, per 1000 atoms: 0.22
  Number of scatterers: 6731
  At special positions: 0
  Unit cell: (61.346, 72.952, 120.205, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     O     662      8.00
     N     575      7.00
     C    2183      6.00
     H    3296      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  98 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 302.1 milliseconds
  

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  802

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 6 sheets defined
      9.8% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.482A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.637A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 409
      removed outlier: 4.166A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'H' and resid 89 through 93
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'H' and resid 61 through 62
      removed outlier: 3.529A  pdb=" N   ARG H  50 " --> pdb=" O   ASP H  61 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54
      removed outlier: 3.530A  pdb=" N   SER L  53 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU L  47 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   TYR L  86 " --> pdb=" O   GLY L 101 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   GLY L 101 " --> pdb=" O   TYR L  86 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   CYS L  88 " --> pdb=" O   GLY L  99 " (cutoff:3.500A)

    87 hydrogen bonds defined for protein.
    207 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: 1.04

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 3296
        1.04 -     1.24: 458
        1.24 -     1.44: 1136
        1.44 -     1.64: 1910
        1.64 -     1.84: 18
  Bond restraints: 6818
  Sorted by residual:
  bond pdb=" N   ASP L   1 "
       pdb=" CA  ASP L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.95e+00
  bond pdb=" N   GLN H   1 "
       pdb=" CA  GLN H   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  bond pdb=" N   GLN H   1 "
       pdb=" H   GLN H   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.32e+00
  bond pdb=" N   ASP L   1 "
       pdb=" H   ASP L   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.29e+00
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.21e+00
  ... (remaining 6813 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 11371
        1.03 -     2.06: 794
        2.06 -     3.08: 44
        3.08 -     4.11: 17
        4.11 -     5.14: 3
  Bond angle restraints: 12229
  Sorted by residual:
  angle pdb=" N   GLY H  26 "
        pdb=" CA  GLY H  26 "
        pdb=" C   GLY H  26 "
      ideal   model   delta    sigma   weight residual
     114.16  119.30   -5.14 2.00e+00 2.50e-01 6.60e+00
  angle pdb=" N   GLY H  57 "
        pdb=" CA  GLY H  57 "
        pdb=" C   GLY H  57 "
      ideal   model   delta    sigma   weight residual
     114.48  111.74    2.74 1.19e+00 7.06e-01 5.31e+00
  angle pdb=" CB  ARG A 346 "
        pdb=" CG  ARG A 346 "
        pdb=" CD  ARG A 346 "
      ideal   model   delta    sigma   weight residual
     111.30  115.18   -3.88 2.30e+00 1.89e-01 2.84e+00
  angle pdb=" CG  ARG A 346 "
        pdb=" CD  ARG A 346 "
        pdb=" NE  ARG A 346 "
      ideal   model   delta    sigma   weight residual
     112.00  115.56   -3.56 2.20e+00 2.07e-01 2.62e+00
  angle pdb=" CA  GLN H   1 "
        pdb=" N   GLN H   1 "
        pdb=" H   GLN H   1 "
      ideal   model   delta    sigma   weight residual
     114.00  109.44    4.56 3.00e+00 1.11e-01 2.31e+00
  ... (remaining 12224 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.28: 2917
       16.28 -    32.56: 282
       32.56 -    48.83: 74
       48.83 -    65.11: 25
       65.11 -    81.39: 7
  Dihedral angle restraints: 3305
    sinusoidal: 1760
      harmonic: 1545
  Sorted by residual:
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   20.07   72.93     1      1.00e+01 1.00e-02 6.78e+01
  dihedral pdb=" CA  GLY H  26 "
           pdb=" C   GLY H  26 "
           pdb=" N   PHE H  27 "
           pdb=" CA  PHE H  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.37   22.63     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  SER H  25 "
           pdb=" C   SER H  25 "
           pdb=" N   GLY H  26 "
           pdb=" CA  GLY H  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.60   20.40     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 3302 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 292
       0.027 -    0.053: 156
       0.053 -    0.080: 35
       0.080 -    0.107: 26
       0.107 -    0.133: 12
  Chirality restraints: 521
  Sorted by residual:
  chirality pdb=" CA  VAL H   2 "
            pdb=" N   VAL H   2 "
            pdb=" C   VAL H   2 "
            pdb=" CB  VAL H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  VAL A 362 "
            pdb=" N   VAL A 362 "
            pdb=" C   VAL A 362 "
            pdb=" CB  VAL A 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  VAL L  58 "
            pdb=" N   VAL L  58 "
            pdb=" C   VAL L  58 "
            pdb=" CB  VAL L  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 518 not shown)

  Planarity restraints: 1031
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 408 "    0.096 9.50e-02 1.11e+02   3.22e-02 1.24e+00
        pdb=" NE  ARG A 408 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 408 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 408 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 408 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG A 408 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG A 408 "    0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG A 408 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 408 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 346 "   -0.079 9.50e-02 1.11e+02   2.68e-02 1.15e+00
        pdb=" NE  ARG A 346 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 346 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 346 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 346 "   -0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG A 346 "    0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG A 346 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG A 346 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 346 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER H 112 "    0.017 5.00e-02 4.00e+02   2.60e-02 1.08e+00
        pdb=" N   PRO H 113 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO H 113 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO H 113 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1028 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 610
        2.21 -     2.81: 13812
        2.81 -     3.41: 16511
        3.41 -     4.00: 21961
        4.00 -     4.60: 32493
  Nonbonded interactions: 85387
  Sorted by model distance:
  nonbonded pdb=" H   LYS A 462 "
            pdb=" OE2 GLU A 465 "
     model   vdw
     1.617 2.450
  nonbonded pdb=" OE1 GLN L  55 "
            pdb=" H   GLY L  56 "
     model   vdw
     1.631 2.450
  nonbonded pdb=" HZ2 LYS A 444 "
            pdb=" O   GLY A 447 "
     model   vdw
     1.648 2.450
  nonbonded pdb=" O   SER H 112 "
            pdb=" HE1 TRP H 115 "
     model   vdw
     1.678 2.450
  nonbonded pdb=" OD1 ASN A 422 "
            pdb=" H   ARG A 454 "
     model   vdw
     1.694 2.450
  ... (remaining 85382 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:             0.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.050
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     7.650
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
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      :  0.003   0.033   3529  Z= 0.122
  Angle     :  0.534   5.138   4802  Z= 0.285
  Chirality :  0.040   0.133    521
  Planarity :  0.004   0.042    615
  Dihedral  : 14.084  81.388   1267
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -3.09 (0.38), residues: 434
  helix: -4.37 (0.55), residues: 26
  sheet: -1.42 (0.44), residues: 133
  loop : -2.23 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 346 
 TYR   0.013   0.001   TYR L  36 
 PHE   0.016   0.001   PHE L  71 
 TRP   0.008   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 3522)
  covalent geometry    : angle       0.52887 ( 4787)
  SS BOND              : bond        0.00594 (    6)
  SS BOND              : angle       1.40232 (   12)
  hydrogen bonds       : bond        0.15057 (   87)
  hydrogen bonds       : angle       8.86800 (  207)
  link_NAG-ASN         : bond        0.00285 (    1)
  link_NAG-ASN         : angle       1.24968 (    3)

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

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

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   45 LEU cc_start: 0.8460 (pt) cc_final: 0.8242 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.2627
  time to fit residues: 22.6582
Evaluate side-chains
  41 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 22 optimal weight:   30.0000
   chunk 37 optimal weight:    7.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.051519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.039964 restraints weight = 77445.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.041972 restraints weight = 33116.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.043302 restraints weight = 18261.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.044176 restraints weight = 11753.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.044704 restraints weight = 8395.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3529  Z= 0.170
  Angle     :  0.545   4.829   4802  Z= 0.296
  Chirality :  0.039   0.137    521
  Planarity :  0.004   0.042    615
  Dihedral  :  5.126  41.258    504
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.37 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  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: -2.93 (0.37), residues: 434
  helix: -4.29 (0.47), residues: 32
  sheet: -0.97 (0.48), residues: 117
  loop : -2.20 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 346 
 TYR   0.011   0.001   TYR L  36 
 PHE   0.017   0.002   PHE L  46 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3522)
  covalent geometry    : angle       0.54230 ( 4787)
  SS BOND              : bond        0.00372 (    6)
  SS BOND              : angle       1.13537 (   12)
  hydrogen bonds       : bond        0.03877 (   87)
  hydrogen bonds       : angle       7.62515 (  207)
  link_NAG-ASN         : bond        0.00056 (    1)
  link_NAG-ASN         : angle       1.29259 (    3)

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

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

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  528 LYS cc_start: 0.9666 (mppt) cc_final: 0.9332 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2126
  time to fit residues: 12.2818
Evaluate side-chains
  32 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:   30.0000
   chunk 22 optimal weight:   20.0000
   chunk 5 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   chunk 2 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3341 r_free = 0.3341 target = 0.050581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.039227 restraints weight = 76425.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.041231 restraints weight = 32526.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.042541 restraints weight = 17832.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.043362 restraints weight = 11369.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.043920 restraints weight = 8170.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3529  Z= 0.167
  Angle     :  0.527   4.728   4802  Z= 0.285
  Chirality :  0.040   0.134    521
  Planarity :  0.004   0.033    615
  Dihedral  :  4.812  29.778    504
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  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: -2.87 (0.38), residues: 434
  helix: -4.23 (0.49), residues: 33
  sheet: -1.07 (0.47), residues: 122
  loop : -2.09 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  63 
 TYR   0.014   0.001   TYR A 508 
 PHE   0.024   0.002   PHE A 392 
 TRP   0.014   0.002   TRP L  35 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3522)
  covalent geometry    : angle       0.52539 ( 4787)
  SS BOND              : bond        0.00551 (    6)
  SS BOND              : angle       0.92526 (   12)
  hydrogen bonds       : bond        0.03760 (   87)
  hydrogen bonds       : angle       7.65051 (  207)
  link_NAG-ASN         : bond        0.00147 (    1)
  link_NAG-ASN         : angle       0.99929 (    3)

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

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

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  528 LYS cc_start: 0.9673 (mppt) cc_final: 0.9403 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.2063
  time to fit residues: 10.4777
Evaluate side-chains
  29 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:   30.0000
   chunk 33 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 20 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    3.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.050540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.039260 restraints weight = 75325.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.041251 restraints weight = 31779.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.042557 restraints weight = 17370.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.043411 restraints weight = 11053.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.043932 restraints weight = 7882.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3529  Z= 0.126
  Angle     :  0.497   4.583   4802  Z= 0.266
  Chirality :  0.040   0.132    521
  Planarity :  0.003   0.035    615
  Dihedral  :  4.460  21.921    504
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.87 %
    Favored  : 97.86 %
  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: -2.67 (0.39), residues: 434
  helix: -3.84 (0.64), residues: 31
  sheet: -1.07 (0.47), residues: 122
  loop : -1.93 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  74 
 TYR   0.007   0.001   TYR A 508 
 PHE   0.013   0.001   PHE L  71 
 TRP   0.010   0.001   TRP L  35 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3522)
  covalent geometry    : angle       0.49468 ( 4787)
  SS BOND              : bond        0.00290 (    6)
  SS BOND              : angle       1.01258 (   12)
  hydrogen bonds       : bond        0.03490 (   87)
  hydrogen bonds       : angle       7.32558 (  207)
  link_NAG-ASN         : bond        0.00247 (    1)
  link_NAG-ASN         : angle       0.94246 (    3)

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

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

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  528 LYS cc_start: 0.9674 (mppt) cc_final: 0.9407 (mmtm)
REVERT: H   56 ASP cc_start: 0.8500 (t0) cc_final: 0.8247 (t0)
REVERT: H  102 ASP cc_start: 0.9047 (t0) cc_final: 0.8379 (m-30)
REVERT: L   97 THR cc_start: 0.8334 (m) cc_final: 0.7679 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 45
  average time/residue: 0.2220
  time to fit residues: 11.5040
Evaluate side-chains
  30 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 29 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
H 117 GLN
L  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.048626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.037606 restraints weight = 80776.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.039511 restraints weight = 34524.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.040813 restraints weight = 18922.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.041629 restraints weight = 11952.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.042116 restraints weight = 8486.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3529  Z= 0.191
  Angle     :  0.538   4.668   4802  Z= 0.290
  Chirality :  0.039   0.132    521
  Planarity :  0.004   0.042    615
  Dihedral  :  4.543  21.899    504
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.83 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  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: -2.57 (0.39), residues: 434
  helix: -2.88 (1.02), residues: 25
  sheet: -1.24 (0.47), residues: 122
  loop : -1.90 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 355 
 TYR   0.009   0.001   TYR A 508 
 PHE   0.015   0.002   PHE L  71 
 TRP   0.008   0.001   TRP L  96 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 3522)
  covalent geometry    : angle       0.53480 ( 4787)
  SS BOND              : bond        0.00183 (    6)
  SS BOND              : angle       1.26214 (   12)
  hydrogen bonds       : bond        0.03401 (   87)
  hydrogen bonds       : angle       7.36447 (  207)
  link_NAG-ASN         : bond        0.00186 (    1)
  link_NAG-ASN         : angle       1.18354 (    3)

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

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

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 ILE cc_start: 0.9652 (mt) cc_final: 0.9365 (tp)
REVERT: A  528 LYS cc_start: 0.9680 (mppt) cc_final: 0.9332 (mmtt)
REVERT: H   56 ASP cc_start: 0.8757 (t0) cc_final: 0.8488 (t0)
REVERT: H  102 ASP cc_start: 0.9062 (t0) cc_final: 0.8311 (m-30)
REVERT: L   97 THR cc_start: 0.8388 (m) cc_final: 0.7814 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.2518
  time to fit residues: 12.0385
Evaluate side-chains
  33 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 23 optimal weight:   20.0000
   chunk 15 optimal weight:    4.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.049134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.037948 restraints weight = 79557.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.039925 restraints weight = 33935.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.041279 restraints weight = 18482.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.042088 restraints weight = 11632.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.042655 restraints weight = 8365.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.4284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3529  Z= 0.144
  Angle     :  0.514   4.305   4802  Z= 0.274
  Chirality :  0.039   0.133    521
  Planarity :  0.004   0.054    615
  Dihedral  :  4.456  22.137    504
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  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: -2.39 (0.40), residues: 434
  helix: -2.92 (0.99), residues: 25
  sheet: -1.19 (0.48), residues: 123
  loop : -1.71 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 454 
 TYR   0.010   0.001   TYR A 508 
 PHE   0.011   0.002   PHE L  71 
 TRP   0.006   0.001   TRP L  35 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3522)
  covalent geometry    : angle       0.50820 ( 4787)
  SS BOND              : bond        0.00359 (    6)
  SS BOND              : angle       1.58900 (   12)
  hydrogen bonds       : bond        0.03216 (   87)
  hydrogen bonds       : angle       7.18901 (  207)
  link_NAG-ASN         : bond        0.00381 (    1)
  link_NAG-ASN         : angle       1.02499 (    3)

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

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

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 ILE cc_start: 0.9630 (mt) cc_final: 0.9340 (tp)
REVERT: A  528 LYS cc_start: 0.9676 (mppt) cc_final: 0.9316 (mmtt)
REVERT: H   56 ASP cc_start: 0.8805 (t0) cc_final: 0.8559 (t70)
REVERT: H  102 ASP cc_start: 0.9026 (t0) cc_final: 0.8252 (m-30)
REVERT: L   97 THR cc_start: 0.8414 (m) cc_final: 0.7877 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.2316
  time to fit residues: 12.7803
Evaluate side-chains
  33 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 14 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.049634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.038735 restraints weight = 76152.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.040692 restraints weight = 32882.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.041982 restraints weight = 17973.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.042777 restraints weight = 11323.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.043304 restraints weight = 8123.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.4453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3529  Z= 0.121
  Angle     :  0.501   4.571   4802  Z= 0.266
  Chirality :  0.040   0.147    521
  Planarity :  0.004   0.036    615
  Dihedral  :  4.389  22.313    504
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.06 %
    Favored  : 88.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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: -2.42 (0.39), residues: 434
  helix: -2.97 (0.95), residues: 25
  sheet: -1.14 (0.48), residues: 122
  loop : -1.76 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 454 
 TYR   0.010   0.001   TYR A 508 
 PHE   0.010   0.001   PHE L  46 
 TRP   0.005   0.001   TRP L  35 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3522)
  covalent geometry    : angle       0.49711 ( 4787)
  SS BOND              : bond        0.00347 (    6)
  SS BOND              : angle       1.21274 (   12)
  hydrogen bonds       : bond        0.03107 (   87)
  hydrogen bonds       : angle       7.03068 (  207)
  link_NAG-ASN         : bond        0.00342 (    1)
  link_NAG-ASN         : angle       1.10851 (    3)

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

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

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 ILE cc_start: 0.9628 (mt) cc_final: 0.9323 (tp)
REVERT: A  528 LYS cc_start: 0.9660 (mppt) cc_final: 0.9414 (mptt)
REVERT: H   56 ASP cc_start: 0.8835 (t0) cc_final: 0.8591 (t0)
REVERT: H  102 ASP cc_start: 0.9033 (t0) cc_final: 0.8272 (m-30)
REVERT: L   97 THR cc_start: 0.8405 (m) cc_final: 0.7872 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.2151
  time to fit residues: 11.2779
Evaluate side-chains
  33 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:   30.0000
   chunk 39 optimal weight:   40.0000
   chunk 35 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 22 optimal weight:   30.0000
   chunk 32 optimal weight:    0.6980
   chunk 34 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    6.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.048715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.037862 restraints weight = 81593.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.039791 restraints weight = 35088.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.041046 restraints weight = 19194.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.041898 restraints weight = 12157.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.042399 restraints weight = 8520.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.4950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3529  Z= 0.196
  Angle     :  0.556   4.177   4802  Z= 0.300
  Chirality :  0.039   0.134    521
  Planarity :  0.005   0.045    615
  Dihedral  :  4.762  22.219    504
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.98 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  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: -2.55 (0.39), residues: 434
  helix: -3.18 (0.75), residues: 31
  sheet: -1.12 (0.48), residues: 121
  loop : -1.85 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 454 
 TYR   0.026   0.001   TYR A 508 
 PHE   0.010   0.002   PHE H  29 
 TRP   0.011   0.002   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 3522)
  covalent geometry    : angle       0.55099 ( 4787)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       1.48399 (   12)
  hydrogen bonds       : bond        0.03406 (   87)
  hydrogen bonds       : angle       7.18446 (  207)
  link_NAG-ASN         : bond        0.00281 (    1)
  link_NAG-ASN         : angle       1.42533 (    3)

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

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

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 ILE cc_start: 0.9672 (mt) cc_final: 0.9394 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.2320
  time to fit residues: 10.0881
Evaluate side-chains
  31 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.049050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.038153 restraints weight = 81980.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.040146 restraints weight = 35586.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.041439 restraints weight = 19562.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.042239 restraints weight = 12358.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.042817 restraints weight = 8850.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.5017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3529  Z= 0.125
  Angle     :  0.507   3.932   4802  Z= 0.271
  Chirality :  0.039   0.133    521
  Planarity :  0.004   0.034    615
  Dihedral  :  4.514  23.275    504
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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: -2.39 (0.40), residues: 434
  helix: -2.99 (0.79), residues: 31
  sheet: -1.09 (0.48), residues: 125
  loop : -1.71 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 454 
 TYR   0.014   0.001   TYR A 508 
 PHE   0.009   0.001   PHE A 392 
 TRP   0.006   0.001   TRP A 353 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3522)
  covalent geometry    : angle       0.50301 ( 4787)
  SS BOND              : bond        0.00590 (    6)
  SS BOND              : angle       1.32713 (   12)
  hydrogen bonds       : bond        0.03054 (   87)
  hydrogen bonds       : angle       6.99113 (  207)
  link_NAG-ASN         : bond        0.00354 (    1)
  link_NAG-ASN         : angle       1.19259 (    3)

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

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

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 ILE cc_start: 0.9631 (mt) cc_final: 0.9355 (tp)
REVERT: A  528 LYS cc_start: 0.9628 (mppt) cc_final: 0.9371 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.2808
  time to fit residues: 13.6836
Evaluate side-chains
  34 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 29 optimal weight:   20.0000
   chunk 12 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 32 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.048330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.037467 restraints weight = 80575.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.039400 restraints weight = 34615.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.040693 restraints weight = 18990.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.041520 restraints weight = 12022.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.042074 restraints weight = 8492.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.5214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3529  Z= 0.151
  Angle     :  0.521   3.926   4802  Z= 0.278
  Chirality :  0.039   0.133    521
  Planarity :  0.004   0.036    615
  Dihedral  :  4.518  21.596    504
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.75 %
    Favored  : 88.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.26 (0.40), residues: 434
  helix: -2.43 (0.99), residues: 25
  sheet: -0.92 (0.49), residues: 121
  loop : -1.76 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 454 
 TYR   0.015   0.001   TYR A 508 
 PHE   0.010   0.002   PHE A 392 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3522)
  covalent geometry    : angle       0.51721 ( 4787)
  SS BOND              : bond        0.00527 (    6)
  SS BOND              : angle       1.31940 (   12)
  hydrogen bonds       : bond        0.03122 (   87)
  hydrogen bonds       : angle       6.92424 (  207)
  link_NAG-ASN         : bond        0.00324 (    1)
  link_NAG-ASN         : angle       1.16827 (    3)

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

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

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  868 Ramachandran restraints generated.
    434 Oldfield, 0 Emsley, 434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 TYR cc_start: 0.9401 (m-10) cc_final: 0.9173 (m-10)
REVERT: A  434 ILE cc_start: 0.9641 (mt) cc_final: 0.9321 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.2878
  time to fit residues: 13.2192
Evaluate side-chains
  35 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 38 optimal weight:   30.0000
   chunk 31 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
L  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.048579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.037658 restraints weight = 81108.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.039628 restraints weight = 34993.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.040940 restraints weight = 19199.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.041799 restraints weight = 12108.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.042358 restraints weight = 8528.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.5375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3529  Z= 0.129
  Angle     :  0.504   3.685   4802  Z= 0.268
  Chirality :  0.039   0.132    521
  Planarity :  0.004   0.035    615
  Dihedral  :  4.428  20.950    504
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.29 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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: -2.22 (0.40), residues: 434
  helix: -2.50 (0.95), residues: 25
  sheet: -0.89 (0.49), residues: 121
  loop : -1.72 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 454 
 TYR   0.015   0.001   TYR A 508 
 PHE   0.010   0.001   PHE A 392 
 TRP   0.006   0.001   TRP A 353 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3522)
  covalent geometry    : angle       0.50046 ( 4787)
  SS BOND              : bond        0.00495 (    6)
  SS BOND              : angle       1.22978 (   12)
  hydrogen bonds       : bond        0.03001 (   87)
  hydrogen bonds       : angle       6.84774 (  207)
  link_NAG-ASN         : bond        0.00341 (    1)
  link_NAG-ASN         : angle       1.16361 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1477.47 seconds
wall clock time: 25 minutes 49.30 seconds (1549.30 seconds total)