Starting phenix.real_space_refine
on Sat Apr 26 20:03:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fgu_50428/04_2025/9fgu_50428.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fgu_50428/04_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_50428/04_2025/9fgu_50428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fgu_50428/04_2025/9fgu_50428.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fgu_50428/04_2025/9fgu_50428.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fgu_50428/04_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-5669/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: 3.99, per 1000 atoms: 1.23
  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: 0.80
  Conformation dependent library (CDL) restraints added in 414.3 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: 0.46
  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: 0.91

  Time building geometry restraints manager: 0.98 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:             3.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     15.010
  Find NCS groups from input model:        0.040
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.160
-------------------------------------------------------------------------------
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  : 0.326 
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: 0.2013
  time to fit residues: 15.7482
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  : 0.372 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    0.1980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.107653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.096219 restraints weight = 11828.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.098661 restraints weight = 7403.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.100347 restraints weight = 5078.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3331  Z= 0.147
  Angle     :  0.709   8.673   4533  Z= 0.365
  Chirality :  0.047   0.162    488
  Planarity :  0.005   0.040    585
  Dihedral  :  6.581  59.681    480
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 17.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  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: -1.19 (0.41), residues: 407
  helix: -0.51 (1.23), residues: 21
  sheet: -0.16 (0.50), residues: 114
  loop : -1.13 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP E 169 
 HIS   0.002   0.001   HIS C 505 
 PHE   0.014   0.002   PHE C 392 
 TYR   0.015   0.001   TYR C 489 
 ARG   0.004   0.001   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00706 (    1)
  link_NAG-ASN         : angle       1.60303 (    3)
  hydrogen bonds       : bond        0.05183 (   70)
  hydrogen bonds       : angle       7.40663 (  204)
  SS BOND              : bond        0.00513 (    5)
  SS BOND              : angle       2.89623 (   10)
  covalent geometry    : bond        0.00324 ( 3325)
  covalent geometry    : angle       0.69587 ( 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
  60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: E  238 ARG cc_start: 0.7367 (mmm-85) cc_final: 0.7074 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1966
  time to fit residues: 13.9532
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0040
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.5992

-------------------------------------------------------------------------------
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
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.107224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.095577 restraints weight = 11760.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.098097 restraints weight = 7103.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.099817 restraints weight = 4780.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3331  Z= 0.136
  Angle     :  0.697   8.453   4533  Z= 0.352
  Chirality :  0.046   0.158    488
  Planarity :  0.004   0.036    585
  Dihedral  :  6.457  59.567    480
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 17.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.41), residues: 407
  helix: -1.10 (1.05), residues: 27
  sheet: -0.32 (0.50), residues: 116
  loop : -1.12 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 169 
 HIS   0.003   0.001   HIS C 505 
 PHE   0.016   0.001   PHE C 392 
 TYR   0.010   0.001   TYR C 508 
 ARG   0.004   0.001   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00641 (    1)
  link_NAG-ASN         : angle       1.76993 (    3)
  hydrogen bonds       : bond        0.04373 (   70)
  hydrogen bonds       : angle       6.71293 (  204)
  SS BOND              : bond        0.00469 (    5)
  SS BOND              : angle       2.66042 (   10)
  covalent geometry    : bond        0.00304 ( 3325)
  covalent geometry    : angle       0.68555 ( 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  : 0.347 
Fit side-chains
REVERT: E   47 TRP cc_start: 0.8692 (t60) cc_final: 0.8374 (t60)
REVERT: E  230 ARG cc_start: 0.8378 (ptp-170) cc_final: 0.8051 (ptp-170)
REVERT: E  238 ARG cc_start: 0.7313 (mmm-85) cc_final: 0.7039 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2138
  time to fit residues: 14.5168
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  : 0.356 
-------------------------------------------------------------------------------
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:    0.0040
   chunk 32 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0060
   chunk 31 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.4408

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

Flipped N/Q/H residues before XYZ refinement:
C 414 GLN
** 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 = 0.3807 r_free = 0.3807 target = 0.108176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.096858 restraints weight = 12401.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.099322 restraints weight = 7515.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.100993 restraints weight = 5076.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.3003

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= 0.119
  Angle     :  0.661   7.560   4533  Z= 0.331
  Chirality :  0.046   0.160    488
  Planarity :  0.004   0.035    585
  Dihedral  :  6.192  58.593    480
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 14.62
  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: -1.23 (0.42), residues: 407
  helix: -1.24 (1.02), residues: 27
  sheet: -0.21 (0.51), residues: 114
  loop : -1.07 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP E 169 
 HIS   0.000   0.000   HIS C 505 
 PHE   0.016   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        0.00584 (    1)
  link_NAG-ASN         : angle       1.73944 (    3)
  hydrogen bonds       : bond        0.03921 (   70)
  hydrogen bonds       : angle       6.26175 (  204)
  SS BOND              : bond        0.00490 (    5)
  SS BOND              : angle       2.50816 (   10)
  covalent geometry    : bond        0.00270 ( 3325)
  covalent geometry    : angle       0.65000 ( 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  : 0.370 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.9055 (tmm160) cc_final: 0.8787 (tmm160)
REVERT: C  444 LYS cc_start: 0.6266 (ttpt) cc_final: 0.5992 (ttpt)
REVERT: E   47 TRP cc_start: 0.8558 (t60) cc_final: 0.8353 (t60)
REVERT: E  230 ARG cc_start: 0.8448 (ptp-170) cc_final: 0.8121 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2099
  time to fit residues: 14.5196
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  : 0.337 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0770
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0980
   chunk 3 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.106761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.095632 restraints weight = 12269.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.098077 restraints weight = 7426.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.099745 restraints weight = 5002.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.3299

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= 0.123
  Angle     :  0.669   7.042   4533  Z= 0.332
  Chirality :  0.046   0.150    488
  Planarity :  0.004   0.036    585
  Dihedral  :  6.179  58.439    480
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  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: -1.36 (0.42), residues: 407
  helix: -1.22 (1.03), residues: 27
  sheet: -0.44 (0.49), residues: 119
  loop : -1.10 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 169 
 HIS   0.005   0.002   HIS C 505 
 PHE   0.015   0.001   PHE C 392 
 TYR   0.008   0.001   TYR C 508 
 ARG   0.006   0.000   ARG E 238 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00584 (    1)
  link_NAG-ASN         : angle       1.77778 (    3)
  hydrogen bonds       : bond        0.03686 (   70)
  hydrogen bonds       : angle       6.53794 (  204)
  SS BOND              : bond        0.00414 (    5)
  SS BOND              : angle       2.50775 (   10)
  covalent geometry    : bond        0.00283 ( 3325)
  covalent geometry    : angle       0.65820 ( 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
  61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.334 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.8978 (tmm160) cc_final: 0.8731 (tmm160)
REVERT: C  444 LYS cc_start: 0.6301 (ttpt) cc_final: 0.6066 (ttpt)
REVERT: E   89 ASP cc_start: 0.4558 (p0) cc_final: 0.4298 (p0)
REVERT: E  230 ARG cc_start: 0.8446 (ptp-170) cc_final: 0.8165 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.2234
  time to fit residues: 15.9748
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  : 0.371 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 1 optimal weight:    0.0470
   chunk 3 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
C 414 GLN
E  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.105253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.094531 restraints weight = 12847.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.096902 restraints weight = 7753.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.098501 restraints weight = 5195.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3331  Z= 0.148
  Angle     :  0.710   7.843   4533  Z= 0.358
  Chirality :  0.046   0.165    488
  Planarity :  0.005   0.036    585
  Dihedral  :  6.343  59.199    480
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  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: -1.46 (0.42), residues: 407
  helix: -1.63 (0.98), residues: 27
  sheet: -0.57 (0.46), residues: 130
  loop : -1.10 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP E 169 
 HIS   0.002   0.001   HIS C 505 
 PHE   0.018   0.002   PHE C 392 
 TYR   0.008   0.001   TYR C 449 
 ARG   0.007   0.001   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00610 (    1)
  link_NAG-ASN         : angle       1.82392 (    3)
  hydrogen bonds       : bond        0.04036 (   70)
  hydrogen bonds       : angle       6.62844 (  204)
  SS BOND              : bond        0.00284 (    5)
  SS BOND              : angle       2.70137 (   10)
  covalent geometry    : bond        0.00342 ( 3325)
  covalent geometry    : angle       0.69829 ( 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
  57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.339 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.9000 (tmm160) cc_final: 0.8761 (tmm160)
REVERT: C  444 LYS cc_start: 0.6293 (ttpt) cc_final: 0.6013 (ttpt)
REVERT: E   89 ASP cc_start: 0.4840 (p0) cc_final: 0.4548 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1970
  time to fit residues: 13.2422
Evaluate side-chains
  41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0050
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0470
   chunk 25 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6096

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.105838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.095313 restraints weight = 12494.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.097563 restraints weight = 7745.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.099095 restraints weight = 5269.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.3852

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= 0.134
  Angle     :  0.700   8.064   4533  Z= 0.348
  Chirality :  0.046   0.177    488
  Planarity :  0.004   0.039    585
  Dihedral  :  6.260  58.315    480
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  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: -1.45 (0.42), residues: 407
  helix: -1.56 (0.97), residues: 27
  sheet: -0.66 (0.45), residues: 132
  loop : -1.05 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP E 169 
 HIS   0.001   0.001   HIS C 505 
 PHE   0.017   0.001   PHE C 392 
 TYR   0.008   0.001   TYR C 508 
 ARG   0.005   0.001   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00576 (    1)
  link_NAG-ASN         : angle       1.89105 (    3)
  hydrogen bonds       : bond        0.03793 (   70)
  hydrogen bonds       : angle       6.45698 (  204)
  SS BOND              : bond        0.00418 (    5)
  SS BOND              : angle       2.51371 (   10)
  covalent geometry    : bond        0.00309 ( 3325)
  covalent geometry    : angle       0.68899 ( 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
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.339 
Fit side-chains
REVERT: C  444 LYS cc_start: 0.6296 (ttpt) cc_final: 0.6013 (ttpt)
REVERT: E   89 ASP cc_start: 0.4972 (p0) cc_final: 0.4750 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1935
  time to fit residues: 12.4617
Evaluate side-chains
  38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 422 ASN
E 223 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.104022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.092911 restraints weight = 12328.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.095305 restraints weight = 7608.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.096977 restraints weight = 5141.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3331  Z= 0.160
  Angle     :  0.732   9.741   4533  Z= 0.364
  Chirality :  0.047   0.197    488
  Planarity :  0.004   0.041    585
  Dihedral  :  6.472  58.403    480
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 17.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  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: -1.53 (0.42), residues: 407
  helix: -1.41 (1.03), residues: 27
  sheet: -0.60 (0.47), residues: 127
  loop : -1.19 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP E 169 
 HIS   0.001   0.000   HIS C 505 
 PHE   0.018   0.002   PHE E  58 
 TYR   0.011   0.001   TYR C 449 
 ARG   0.005   0.001   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00638 (    1)
  link_NAG-ASN         : angle       1.97952 (    3)
  hydrogen bonds       : bond        0.03978 (   70)
  hydrogen bonds       : angle       6.66174 (  204)
  SS BOND              : bond        0.00447 (    5)
  SS BOND              : angle       2.56068 (   10)
  covalent geometry    : bond        0.00372 ( 3325)
  covalent geometry    : angle       0.72137 ( 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
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.393 
Fit side-chains
REVERT: C  444 LYS cc_start: 0.6227 (ttpt) cc_final: 0.5973 (ttpt)
REVERT: E   89 ASP cc_start: 0.5239 (p0) cc_final: 0.5034 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1973
  time to fit residues: 12.2347
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  : 0.339 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0770
   chunk 40 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 9 optimal weight:    0.3980
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.106735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.096068 restraints weight = 12563.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.098410 restraints weight = 7792.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.100004 restraints weight = 5227.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.4188

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= 0.124
  Angle     :  0.698   8.185   4533  Z= 0.347
  Chirality :  0.046   0.170    488
  Planarity :  0.004   0.040    585
  Dihedral  :  6.190  57.751    480
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 14.30
  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: -1.44 (0.42), residues: 407
  helix: -0.47 (1.22), residues: 22
  sheet: -0.66 (0.46), residues: 132
  loop : -1.17 (0.40), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E 169 
 HIS   0.021   0.007   HIS C 505 
 PHE   0.011   0.001   PHE C 347 
 TYR   0.007   0.001   TYR C 508 
 ARG   0.004   0.001   ARG C 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00551 (    1)
  link_NAG-ASN         : angle       1.94186 (    3)
  hydrogen bonds       : bond        0.03603 (   70)
  hydrogen bonds       : angle       6.39111 (  204)
  SS BOND              : bond        0.00434 (    5)
  SS BOND              : angle       2.44833 (   10)
  covalent geometry    : bond        0.00286 ( 3325)
  covalent geometry    : angle       0.68805 ( 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
  57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.332 
Fit side-chains
REVERT: C  444 LYS cc_start: 0.6310 (ttpt) cc_final: 0.6052 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1888
  time to fit residues: 12.7613
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  : 0.431 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0970
   chunk 1 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 38 optimal weight:    0.4980
   chunk 35 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.106190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.095182 restraints weight = 12622.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.097531 restraints weight = 7821.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.099174 restraints weight = 5349.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.4348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3331  Z= 0.133
  Angle     :  0.697   7.304   4533  Z= 0.346
  Chirality :  0.046   0.194    488
  Planarity :  0.004   0.039    585
  Dihedral  :  6.198  57.888    480
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  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: -1.40 (0.42), residues: 407
  helix: -1.44 (0.98), residues: 28
  sheet: -0.59 (0.47), residues: 129
  loop : -1.04 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 169 
 HIS   0.002   0.001   HIS C 505 
 PHE   0.017   0.001   PHE E  58 
 TYR   0.008   0.001   TYR E 183 
 ARG   0.004   0.001   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00580 (    1)
  link_NAG-ASN         : angle       1.96727 (    3)
  hydrogen bonds       : bond        0.03611 (   70)
  hydrogen bonds       : angle       6.38832 (  204)
  SS BOND              : bond        0.00432 (    5)
  SS BOND              : angle       2.44889 (   10)
  covalent geometry    : bond        0.00309 ( 3325)
  covalent geometry    : angle       0.68634 ( 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
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.384 
Fit side-chains
REVERT: C  444 LYS cc_start: 0.6249 (ttpt) cc_final: 0.6011 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.2112
  time to fit residues: 13.0239
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  : 0.335 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 40 optimal weight:    0.0170
   chunk 39 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7018

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.105128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.093482 restraints weight = 12288.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.095960 restraints weight = 7516.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.097678 restraints weight = 5104.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.4390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3331  Z= 0.146
  Angle     :  0.717   7.874   4533  Z= 0.358
  Chirality :  0.047   0.206    488
  Planarity :  0.004   0.039    585
  Dihedral  :  6.350  58.106    480
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  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: -1.49 (0.42), residues: 407
  helix: -1.48 (0.96), residues: 28
  sheet: -0.57 (0.48), residues: 126
  loop : -1.15 (0.40), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP E 169 
 HIS   0.019   0.007   HIS C 505 
 PHE   0.013   0.001   PHE E 233 
 TYR   0.009   0.001   TYR E 183 
 ARG   0.004   0.001   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00594 (    1)
  link_NAG-ASN         : angle       2.10925 (    3)
  hydrogen bonds       : bond        0.03860 (   70)
  hydrogen bonds       : angle       6.63848 (  204)
  SS BOND              : bond        0.00455 (    5)
  SS BOND              : angle       2.41386 (   10)
  covalent geometry    : bond        0.00338 ( 3325)
  covalent geometry    : angle       0.70642 ( 4520)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1666.28 seconds
wall clock time: 29 minutes 30.81 seconds (1770.81 seconds total)