Starting phenix.real_space_refine
on Fri May  9 17:35:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fgu_50428/05_2025/9fgu_50428.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fgu_50428/05_2025/9fgu_50428.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fgu_50428/05_2025/9fgu_50428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fgu_50428/05_2025/9fgu_50428.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fgu_50428/05_2025/9fgu_50428.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fgu_50428/05_2025/9fgu_50428.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.004 sd=   0.035
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      13      5.16       5
     C    2071      2.51       5
     N     545      2.21       5
     O     612      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3241
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1541
          Classifications: {'peptide': 191}
          Link IDs: {'PTRANS': 11, 'TRANS': 179}
    Chain: "E"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1686
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.81, per 1000 atoms: 1.18
  Number of scatterers: 3241
  At special positions: 0
  Unit cell: (80.01, 64.897, 92.456, 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      13     16.00
     O     612      8.00
     N     545      7.00
     C    2071      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 156 " - pdb=" SG  CYS E 222 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG C1301 " - " ASN C 343 "
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 392.9 milliseconds
  

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  754

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      11.6% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'C' and resid 383 through 389
      removed outlier: 3.889A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 410
      removed outlier: 3.641A  pdb=" N   ARG C 408 " --> pdb=" O   GLY C 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 438 through 443
    Processing helix  chain 'C' and resid 479 through 483
      removed outlier: 3.836A  pdb=" N   GLY C 482 " --> pdb=" O   PRO C 479 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 163 through 165
      No H-bonds generated for 'chain 'E' and resid 163 through 165'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.633A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER C 399 " --> pdb=" O   ASN C 354 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 5
      removed outlier: 3.860A  pdb=" N   TYR E  79 " --> pdb=" O   SER E  70 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59
      removed outlier: 5.949A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   MET E  34 " --> pdb=" O   ILE E  51 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG E  97 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   ILE E 107 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 57 through 59
      removed outlier: 5.949A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   MET E  34 " --> pdb=" O   ILE E  51 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 138 through 139
      removed outlier: 3.509A  pdb=" N   CYS E 156 " --> pdb=" O   PHE E 205 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   THR E 208 " --> pdb=" O   SER E 197 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 144 through 145
      removed outlier: 6.289A  pdb=" N   LEU E 144 " --> pdb=" O   GLU E 240 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE E 219 " --> pdb=" O   GLN E 172 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   TYR E 221 " --> pdb=" O   TYR E 170 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   TYR E 170 " --> pdb=" O   TYR E 221 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   LEU E 167 " --> pdb=" O   ILE E 182 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   ILE E 182 " --> pdb=" O   LEU E 167 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   TRP E 169 " --> pdb=" O   LEU E 180 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   LEU E 180 " --> pdb=" O   TRP E 169 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   GLN E 171 " --> pdb=" O   PRO E 178 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LYS E 173 " --> pdb=" O   GLN E 176 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 144 through 145
      removed outlier: 6.289A  pdb=" N   LEU E 144 " --> pdb=" O   GLU E 240 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLU E 224 " --> pdb=" O   THR E 232 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   THR E 232 " --> pdb=" O   GLU E 224 " (cutoff:3.500A)

    84 hydrogen bonds defined for protein.
    204 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.84

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1037
        1.34 -     1.46: 864
        1.46 -     1.58: 1409
        1.58 -     1.70: 0
        1.70 -     1.81: 15
  Bond restraints: 3325
  Sorted by residual:
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.68e+00
  bond pdb=" CB  ASP C 428 "
       pdb=" CG  ASP C 428 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.46e+00
  bond pdb=" C5  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  bond pdb=" CA  ASP C 428 "
       pdb=" CB  ASP C 428 "
    ideal  model  delta    sigma   weight residual
    1.532  1.546 -0.014 1.33e-02 5.65e+03 1.14e+00
  bond pdb=" C3  NAG C1301 "
       pdb=" O3  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.403  1.422 -0.019 2.00e-02 2.50e+03 9.39e-01
  ... (remaining 3320 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 4226
        1.28 -     2.57: 231
        2.57 -     3.85: 49
        3.85 -     5.13: 8
        5.13 -     6.42: 6
  Bond angle restraints: 4520
  Sorted by residual:
  angle pdb=" N   GLY C 431 "
        pdb=" CA  GLY C 431 "
        pdb=" C   GLY C 431 "
      ideal   model   delta    sigma   weight residual
     112.04  106.92    5.12 1.02e+00 9.61e-01 2.52e+01
  angle pdb=" CA  GLY C 431 "
        pdb=" C   GLY C 431 "
        pdb=" O   GLY C 431 "
      ideal   model   delta    sigma   weight residual
     122.45  118.86    3.59 7.20e-01 1.93e+00 2.49e+01
  angle pdb=" N   CYS C 432 "
        pdb=" CA  CYS C 432 "
        pdb=" C   CYS C 432 "
      ideal   model   delta    sigma   weight residual
     108.38  114.61   -6.23 1.35e+00 5.49e-01 2.13e+01
  angle pdb=" CA  GLY C 431 "
        pdb=" C   GLY C 431 "
        pdb=" N   CYS C 432 "
      ideal   model   delta    sigma   weight residual
     114.29  119.03   -4.74 1.41e+00 5.03e-01 1.13e+01
  angle pdb=" N   ALA E 218 "
        pdb=" CA  ALA E 218 "
        pdb=" C   ALA E 218 "
      ideal   model   delta    sigma   weight residual
     107.88  112.26   -4.38 1.41e+00 5.03e-01 9.64e+00
  ... (remaining 4515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 1762
       17.27 -    34.54: 162
       34.54 -    51.81: 25
       51.81 -    69.07: 9
       69.07 -    86.34: 6
  Dihedral angle restraints: 1964
    sinusoidal: 773
      harmonic: 1191
  Sorted by residual:
  dihedral pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.47   63.47     1      1.00e+01 1.00e-02 5.31e+01
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -26.72  -59.28     1      1.00e+01 1.00e-02 4.70e+01
  dihedral pdb=" CA  CYS C 379 "
           pdb=" C   CYS C 379 "
           pdb=" N   TYR C 380 "
           pdb=" CA  TYR C 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.46  -23.54     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 1961 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 299
       0.033 -    0.066: 115
       0.066 -    0.098: 43
       0.098 -    0.131: 30
       0.131 -    0.164: 1
  Chirality restraints: 488
  Sorted by residual:
  chirality pdb=" CG  LEU E  85 "
            pdb=" CB  LEU E  85 "
            pdb=" CD1 LEU E  85 "
            pdb=" CD2 LEU E  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.72e-01
  chirality pdb=" CA  ILE C 434 "
            pdb=" N   ILE C 434 "
            pdb=" C   ILE C 434 "
            pdb=" CB  ILE C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.27e-01
  chirality pdb=" CA  ASP C 428 "
            pdb=" N   ASP C 428 "
            pdb=" C   ASP C 428 "
            pdb=" CB  ASP C 428 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 485 not shown)

  Planarity restraints: 586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 478 "    0.031 5.00e-02 4.00e+02   4.73e-02 3.58e+00
        pdb=" N   PRO C 479 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C 479 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 479 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 108 "    0.008 2.00e-02 2.50e+03   9.29e-03 2.16e+00
        pdb=" CG  TRP E 108 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 108 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 108 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 108 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 108 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 108 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 108 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 108 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 108 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E 192 "   -0.020 5.00e-02 4.00e+02   2.95e-02 1.40e+00
        pdb=" N   PRO E 193 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO E 193 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E 193 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 583 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 87
        2.68 -     3.23: 3289
        3.23 -     3.79: 4956
        3.79 -     4.34: 6344
        4.34 -     4.90: 9980
  Nonbonded interactions: 24656
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 364 "
            pdb=" OG  SER C 366 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" OG1 THR E  90 "
            pdb=" O   VAL E 114 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   TRP C 353 "
            pdb=" NH2 ARG C 466 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" NE2 GLN E  39 "
            pdb=" O   LYS E  43 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" NH1 ARG E 211 "
            pdb=" O   LEU E 212 "
     model   vdw
     2.260 3.120
  ... (remaining 24651 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=0.00 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:             2.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.940
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.010
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
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   3331  Z= 0.165
  Angle     :  0.727   6.419   4533  Z= 0.411
  Chirality :  0.045   0.164    488
  Planarity :  0.004   0.047    585
  Dihedral  : 13.955  86.342   1195
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 19.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.86 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.40), residues: 407
  helix: -1.17 (1.14), residues: 20
  sheet: -0.09 (0.51), residues: 111
  loop : -1.25 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E 108 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.019   0.002   PHE E  58 
 TYR   0.009   0.001   TYR C 365 
 ARG   0.003   0.000   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00541 (    1)
  link_NAG-ASN         : angle       1.93126 (    3)
  hydrogen bonds       : bond        0.30921 (   70)
  hydrogen bonds       : angle      10.67441 (  204)
  SS BOND              : bond        0.00517 (    5)
  SS BOND              : angle       2.71581 (   10)
  covalent geometry    : bond        0.00333 ( 3325)
  covalent geometry    : angle       0.71541 ( 4520)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.344 
Fit side-chains
REVERT: E  238 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7604 (ttm110)
  outliers start: 1
  outliers final: 1
  residues processed: 66
  average time/residue: 0.2007
  time to fit residues: 15.6747
Evaluate side-chains
  38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0070
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    0.1980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
C 414 GLN
** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 505 HIS
E  76 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.108556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.097760 restraints weight = 12146.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.100014 restraints weight = 7787.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.101580 restraints weight = 5401.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3331  Z= 0.132
  Angle     :  0.698   8.762   4533  Z= 0.357
  Chirality :  0.047   0.164    488
  Planarity :  0.004   0.039    585
  Dihedral  :  6.516  59.910    480
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 16.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.41), residues: 407
  helix: -0.57 (1.20), residues: 21
  sheet: -0.15 (0.50), residues: 114
  loop : -1.11 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E 169 
 HIS   0.002   0.001   HIS C 505 
 PHE   0.013   0.001   PHE C 392 
 TYR   0.014   0.001   TYR C 489 
 ARG   0.003   0.001   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00661 (    1)
  link_NAG-ASN         : angle       1.55574 (    3)
  hydrogen bonds       : bond        0.04986 (   70)
  hydrogen bonds       : angle       7.30841 (  204)
  SS BOND              : bond        0.00503 (    5)
  SS BOND              : angle       2.83614 (   10)
  covalent geometry    : bond        0.00296 ( 3325)
  covalent geometry    : angle       0.68528 ( 4520)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: C  471 GLU cc_start: 0.6411 (pm20) cc_final: 0.6052 (pm20)
REVERT: E  238 ARG cc_start: 0.7310 (mmm-85) cc_final: 0.7065 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1995
  time to fit residues: 14.3526
Evaluate side-chains
  40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    0.3980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
C 414 GLN
** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 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 = 0.3758 r_free = 0.3758 target = 0.104894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.094057 restraints weight = 12224.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.096310 restraints weight = 7650.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.097862 restraints weight = 5268.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3331  Z= 0.161
  Angle     :  0.719   8.621   4533  Z= 0.364
  Chirality :  0.047   0.162    488
  Planarity :  0.004   0.036    585
  Dihedral  :  6.660  59.908    480
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 19.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.41), residues: 407
  helix: -1.31 (1.01), residues: 27
  sheet: -0.58 (0.46), residues: 132
  loop : -1.21 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 169 
 HIS   0.001   0.001   HIS C 505 
 PHE   0.018   0.001   PHE C 392 
 TYR   0.010   0.002   TYR C 508 
 ARG   0.004   0.001   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00680 (    1)
  link_NAG-ASN         : angle       1.83418 (    3)
  hydrogen bonds       : bond        0.04583 (   70)
  hydrogen bonds       : angle       6.78203 (  204)
  SS BOND              : bond        0.00488 (    5)
  SS BOND              : angle       2.74346 (   10)
  covalent geometry    : bond        0.00361 ( 3325)
  covalent geometry    : angle       0.70703 ( 4520)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.349 
Fit side-chains
REVERT: C  444 LYS cc_start: 0.6385 (ttpt) cc_final: 0.6070 (ttpt)
REVERT: C  465 GLU cc_start: 0.8512 (tp30) cc_final: 0.8179 (tp30)
REVERT: E  238 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.7044 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2094
  time to fit residues: 14.2183
Evaluate side-chains
  43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    0.0870
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0670
   chunk 37 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0170
   chunk 31 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.3734

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

Flipped N/Q/H residues before XYZ refinement:
C 394 ASN
C 414 GLN
C 505 HIS
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.108844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.097035 restraints weight = 12046.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.099617 restraints weight = 7245.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.101352 restraints weight = 4847.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3331  Z= 0.118
  Angle     :  0.665   7.651   4533  Z= 0.331
  Chirality :  0.046   0.161    488
  Planarity :  0.004   0.036    585
  Dihedral  :  6.175  58.616    480
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.41), residues: 407
  helix: -1.25 (1.02), residues: 27
  sheet: -0.36 (0.50), residues: 117
  loop : -1.10 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP E 169 
 HIS   0.001   0.000   HIS C 505 
 PHE   0.015   0.001   PHE E  58 
 TYR   0.010   0.001   TYR C 508 
 ARG   0.003   0.000   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00576 (    1)
  link_NAG-ASN         : angle       1.73272 (    3)
  hydrogen bonds       : bond        0.03942 (   70)
  hydrogen bonds       : angle       6.21396 (  204)
  SS BOND              : bond        0.01011 (    5)
  SS BOND              : angle       2.50628 (   10)
  covalent geometry    : bond        0.00262 ( 3325)
  covalent geometry    : angle       0.65441 ( 4520)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.360 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.9048 (tmm160) cc_final: 0.8788 (tmm160)
REVERT: C  444 LYS cc_start: 0.6183 (ttpt) cc_final: 0.5910 (ttpt)
REVERT: E   47 TRP cc_start: 0.8647 (t60) cc_final: 0.8420 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1847
  time to fit residues: 12.9749
Evaluate side-chains
  43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.106188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.095008 restraints weight = 12729.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.097436 restraints weight = 7768.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.099117 restraints weight = 5267.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.3336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3331  Z= 0.134
  Angle     :  0.681   6.975   4533  Z= 0.339
  Chirality :  0.046   0.158    488
  Planarity :  0.004   0.036    585
  Dihedral  :  6.288  58.722    480
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.41), residues: 407
  helix: -1.20 (1.04), residues: 27
  sheet: -0.47 (0.50), residues: 117
  loop : -1.13 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 169 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.019   0.001   PHE C 392 
 TYR   0.009   0.001   TYR C 453 
 ARG   0.003   0.000   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00617 (    1)
  link_NAG-ASN         : angle       1.82926 (    3)
  hydrogen bonds       : bond        0.03878 (   70)
  hydrogen bonds       : angle       6.67226 (  204)
  SS BOND              : bond        0.00488 (    5)
  SS BOND              : angle       2.47840 (   10)
  covalent geometry    : bond        0.00302 ( 3325)
  covalent geometry    : angle       0.67004 ( 4520)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.388 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.9013 (tmm160) cc_final: 0.8757 (tmm160)
REVERT: C  444 LYS cc_start: 0.6227 (ttpt) cc_final: 0.5876 (ttpt)
REVERT: E   89 ASP cc_start: 0.4612 (p0) cc_final: 0.4304 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2190
  time to fit residues: 14.9778
Evaluate side-chains
  39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.0870
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    0.2980
   chunk 26 optimal weight:    0.0020
   chunk 11 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.3766

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

Flipped N/Q/H residues before XYZ refinement:
E  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.108050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.096872 restraints weight = 12836.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.099353 restraints weight = 7683.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.101053 restraints weight = 5149.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3331  Z= 0.116
  Angle     :  0.675   7.871   4533  Z= 0.336
  Chirality :  0.045   0.156    488
  Planarity :  0.004   0.035    585
  Dihedral  :  6.091  58.537    480
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.41), residues: 407
  helix: -1.25 (1.02), residues: 27
  sheet: -0.46 (0.49), residues: 119
  loop : -1.04 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP E 169 
 HIS   0.004   0.001   HIS C 505 
 PHE   0.017   0.001   PHE E  58 
 TYR   0.007   0.001   TYR C 501 
 ARG   0.006   0.000   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00538 (    1)
  link_NAG-ASN         : angle       1.77038 (    3)
  hydrogen bonds       : bond        0.03661 (   70)
  hydrogen bonds       : angle       6.45796 (  204)
  SS BOND              : bond        0.00209 (    5)
  SS BOND              : angle       2.55300 (   10)
  covalent geometry    : bond        0.00261 ( 3325)
  covalent geometry    : angle       0.66316 ( 4520)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.368 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.8998 (tmm160) cc_final: 0.8725 (tmm160)
REVERT: C  444 LYS cc_start: 0.6262 (ttpt) cc_final: 0.5894 (ttpt)
REVERT: E  230 ARG cc_start: 0.8389 (ptp-170) cc_final: 0.8154 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1882
  time to fit residues: 13.4098
Evaluate side-chains
  42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 2 optimal weight:    0.2980
   chunk 40 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 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 = 0.3743 r_free = 0.3743 target = 0.104869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.093526 restraints weight = 12225.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.096016 restraints weight = 7370.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.097677 restraints weight = 4933.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3331  Z= 0.148
  Angle     :  0.696   7.820   4533  Z= 0.348
  Chirality :  0.046   0.167    488
  Planarity :  0.004   0.036    585
  Dihedral  :  6.325  58.647    480
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.42), residues: 407
  helix: -1.14 (1.05), residues: 27
  sheet: -0.73 (0.46), residues: 129
  loop : -1.14 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP E 169 
 HIS   0.001   0.000   HIS C 505 
 PHE   0.021   0.002   PHE C 392 
 TYR   0.010   0.001   TYR C 449 
 ARG   0.006   0.001   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00623 (    1)
  link_NAG-ASN         : angle       1.94323 (    3)
  hydrogen bonds       : bond        0.03762 (   70)
  hydrogen bonds       : angle       6.54824 (  204)
  SS BOND              : bond        0.00413 (    5)
  SS BOND              : angle       2.57056 (   10)
  covalent geometry    : bond        0.00341 ( 3325)
  covalent geometry    : angle       0.68448 ( 4520)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.409 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.9039 (tmm160) cc_final: 0.8812 (tmm160)
REVERT: E   64 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8946 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1949
  time to fit residues: 13.8885
Evaluate side-chains
  39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 26 optimal weight:    0.3980
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 38 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0770
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0470
   overall best weight:    0.3436

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

Flipped N/Q/H residues before XYZ refinement:
E 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.108065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.096900 restraints weight = 12380.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.099339 restraints weight = 7559.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.100986 restraints weight = 5120.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.4075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3331  Z= 0.115
  Angle     :  0.683   9.011   4533  Z= 0.333
  Chirality :  0.045   0.152    488
  Planarity :  0.004   0.039    585
  Dihedral  :  6.094  57.808    480
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.42), residues: 407
  helix: -1.03 (1.04), residues: 27
  sheet: -0.65 (0.45), residues: 132
  loop : -1.09 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 169 
 HIS   0.001   0.000   HIS C 505 
 PHE   0.018   0.001   PHE E  58 
 TYR   0.008   0.001   TYR C 508 
 ARG   0.004   0.000   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00522 (    1)
  link_NAG-ASN         : angle       1.85631 (    3)
  hydrogen bonds       : bond        0.03439 (   70)
  hydrogen bonds       : angle       6.23744 (  204)
  SS BOND              : bond        0.00463 (    5)
  SS BOND              : angle       2.41004 (   10)
  covalent geometry    : bond        0.00263 ( 3325)
  covalent geometry    : angle       0.67313 ( 4520)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.355 
Fit side-chains
REVERT: C  453 TYR cc_start: 0.7351 (p90) cc_final: 0.7145 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1931
  time to fit residues: 12.8876
Evaluate side-chains
  36 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0770
   chunk 16 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0970
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.3980
   chunk 40 optimal weight:    0.0980
   chunk 15 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.1736

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.110461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.099381 restraints weight = 12638.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.101795 restraints weight = 7714.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.103473 restraints weight = 5231.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3331  Z= 0.111
  Angle     :  0.680   9.241   4533  Z= 0.333
  Chirality :  0.046   0.153    488
  Planarity :  0.004   0.037    585
  Dihedral  :  5.854  56.337    480
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.41), residues: 407
  helix: -1.14 (1.43), residues: 14
  sheet: -0.59 (0.45), residues: 131
  loop : -1.03 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 169 
 HIS   0.010   0.003   HIS C 505 
 PHE   0.011   0.001   PHE E 217 
 TYR   0.009   0.001   TYR E 220 
 ARG   0.003   0.000   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00371 (    1)
  link_NAG-ASN         : angle       2.15095 (    3)
  hydrogen bonds       : bond        0.03417 (   70)
  hydrogen bonds       : angle       6.13211 (  204)
  SS BOND              : bond        0.00386 (    5)
  SS BOND              : angle       2.25374 (   10)
  covalent geometry    : bond        0.00251 ( 3325)
  covalent geometry    : angle       0.67047 ( 4520)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.377 
Fit side-chains
REVERT: C  453 TYR cc_start: 0.7266 (p90) cc_final: 0.7035 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1784
  time to fit residues: 13.0821
Evaluate side-chains
  39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 12 optimal weight:    0.3980
   chunk 24 optimal weight:    0.1980
   chunk 20 optimal weight:    0.4980
   chunk 1 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0370
   chunk 38 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.3658

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.108857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.097938 restraints weight = 12095.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.100315 restraints weight = 7454.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.101901 restraints weight = 5068.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3331  Z= 0.113
  Angle     :  0.679   9.427   4533  Z= 0.331
  Chirality :  0.045   0.156    488
  Planarity :  0.004   0.036    585
  Dihedral  :  5.884  57.561    480
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.42), residues: 407
  helix: -1.02 (1.49), residues: 14
  sheet: -0.52 (0.46), residues: 133
  loop : -1.04 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 169 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.016   0.001   PHE E  58 
 TYR   0.007   0.001   TYR E 183 
 ARG   0.003   0.000   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00505 (    1)
  link_NAG-ASN         : angle       1.62904 (    3)
  hydrogen bonds       : bond        0.03373 (   70)
  hydrogen bonds       : angle       6.07733 (  204)
  SS BOND              : bond        0.00391 (    5)
  SS BOND              : angle       2.22736 (   10)
  covalent geometry    : bond        0.00260 ( 3325)
  covalent geometry    : angle       0.67025 ( 4520)

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

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

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  814 Ramachandran restraints generated.
    407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.345 
Fit side-chains
REVERT: C  453 TYR cc_start: 0.7286 (p90) cc_final: 0.7084 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1885
  time to fit residues: 12.4345
Evaluate side-chains
  39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.0970
   chunk 40 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.106752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.095712 restraints weight = 12258.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.098140 restraints weight = 7468.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.099826 restraints weight = 5062.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.4380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3331  Z= 0.126
  Angle     :  0.700   9.857   4533  Z= 0.342
  Chirality :  0.045   0.160    488
  Planarity :  0.004   0.037    585
  Dihedral  :  6.019  57.239    480
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.42), residues: 407
  helix: -1.33 (1.18), residues: 20
  sheet: -0.53 (0.47), residues: 128
  loop : -1.10 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 169 
 HIS   0.010   0.003   HIS C 505 
 PHE   0.010   0.001   PHE C 347 
 TYR   0.008   0.001   TYR E 183 
 ARG   0.003   0.000   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00568 (    1)
  link_NAG-ASN         : angle       1.68254 (    3)
  hydrogen bonds       : bond        0.03460 (   70)
  hydrogen bonds       : angle       6.14912 (  204)
  SS BOND              : bond        0.00409 (    5)
  SS BOND              : angle       2.29630 (   10)
  covalent geometry    : bond        0.00289 ( 3325)
  covalent geometry    : angle       0.69122 ( 4520)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1648.30 seconds
wall clock time: 29 minutes 27.53 seconds (1767.53 seconds total)