Starting phenix.real_space_refine
on Fri Aug 22 13:26:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fgu_50428/08_2025/9fgu_50428.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fgu_50428/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fgu_50428/08_2025/9fgu_50428.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fgu_50428/08_2025/9fgu_50428.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fgu_50428/08_2025/9fgu_50428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fgu_50428/08_2025/9fgu_50428.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.004 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.28, per 1000 atoms: 0.39
  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: 0.27
  Conformation dependent library (CDL) restraints added in 128.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.14
  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: 0.55

  Time building geometry restraints manager: 0.39 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:             6.430
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.710
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.820
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG E 195 
 TYR   0.009   0.001   TYR C 365 
 PHE   0.019   0.002   PHE E  58 
 TRP   0.024   0.002   TRP E 108 
 HIS   0.001   0.001   HIS C 519 

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

*********************** 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  : 0.151 
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: 0.0796
  time to fit residues: 6.1551
Evaluate side-chains
  39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.3980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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
C 505 HIS
E  76 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.108556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.097688 restraints weight = 12384.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.099937 restraints weight = 7885.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.101477 restraints weight = 5488.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.102670 restraints weight = 4086.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.103494 restraints weight = 3160.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.2083

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     :  0.698   9.091   4533  Z= 0.356
  Chirality :  0.047   0.165    488
  Planarity :  0.004   0.039    585
  Dihedral  :  6.489  59.779    480
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.15 (0.41), residues: 407
  helix: -0.98 (1.02), residues: 27
  sheet: -0.13 (0.50), residues: 114
  loop : -1.05 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 195 
 TYR   0.015   0.001   TYR C 489 
 PHE   0.013   0.001   PHE C 392 
 TRP   0.024   0.002   TRP E 169 
 HIS   0.002   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3325)
  covalent geometry    : angle       0.68538 ( 4520)
  SS BOND              : bond        0.00499 (    5)
  SS BOND              : angle       2.82446 (   10)
  hydrogen bonds       : bond        0.04949 (   70)
  hydrogen bonds       : angle       7.21614 (  204)
  link_NAG-ASN         : bond        0.00687 (    1)
  link_NAG-ASN         : angle       1.53663 (    3)

*********************** 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  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: C  471 GLU cc_start: 0.6396 (pm20) cc_final: 0.6080 (pm20)
REVERT: E  238 ARG cc_start: 0.7252 (mmm-85) cc_final: 0.7049 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0876
  time to fit residues: 6.2045
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  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 10 optimal weight:    0.4980
   chunk 2 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 505 HIS
** 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 = 0.3791 r_free = 0.3791 target = 0.107274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.095910 restraints weight = 12440.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.098299 restraints weight = 7725.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.099932 restraints weight = 5271.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.101074 restraints weight = 3876.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.101907 restraints weight = 3008.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3331  Z= 0.141
  Angle     :  0.695   8.513   4533  Z= 0.352
  Chirality :  0.046   0.156    488
  Planarity :  0.004   0.037    585
  Dihedral  :  6.486  59.596    480
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.41), residues: 407
  helix: -1.14 (1.05), residues: 27
  sheet: -0.34 (0.51), residues: 114
  loop : -1.15 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  19 
 TYR   0.011   0.001   TYR C 508 
 PHE   0.016   0.001   PHE C 392 
 TRP   0.014   0.002   TRP E 169 
 HIS   0.002   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3325)
  covalent geometry    : angle       0.68287 ( 4520)
  SS BOND              : bond        0.00466 (    5)
  SS BOND              : angle       2.67361 (   10)
  hydrogen bonds       : bond        0.04427 (   70)
  hydrogen bonds       : angle       6.71457 (  204)
  link_NAG-ASN         : bond        0.00644 (    1)
  link_NAG-ASN         : angle       1.77695 (    3)

*********************** 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
  61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.131 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.9018 (tmm160) cc_final: 0.8797 (tmm160)
REVERT: E   47 TRP cc_start: 0.8639 (t60) cc_final: 0.8363 (t60)
REVERT: E  230 ARG cc_start: 0.8238 (ptp-170) cc_final: 0.7931 (ptp-170)
REVERT: E  238 ARG cc_start: 0.7231 (mmm-85) cc_final: 0.6989 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0988
  time to fit residues: 6.9776
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  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0670
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0670
   overall best weight:    0.4856

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.107821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.096591 restraints weight = 12497.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.098954 restraints weight = 7628.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.100589 restraints weight = 5158.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.101732 restraints weight = 3765.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.102560 restraints weight = 2904.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.3089

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= 0.125
  Angle     :  0.668   7.631   4533  Z= 0.334
  Chirality :  0.046   0.159    488
  Planarity :  0.004   0.036    585
  Dihedral  :  6.250  58.796    480
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.41), residues: 407
  helix: -1.22 (1.04), residues: 27
  sheet: -0.34 (0.50), residues: 117
  loop : -1.11 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 454 
 TYR   0.010   0.001   TYR C 508 
 PHE   0.014   0.001   PHE E  58 
 TRP   0.030   0.002   TRP E 169 
 HIS   0.003   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3325)
  covalent geometry    : angle       0.65691 ( 4520)
  SS BOND              : bond        0.00525 (    5)
  SS BOND              : angle       2.54247 (   10)
  hydrogen bonds       : bond        0.03989 (   70)
  hydrogen bonds       : angle       6.34457 (  204)
  link_NAG-ASN         : bond        0.00597 (    1)
  link_NAG-ASN         : angle       1.76094 (    3)

*********************** 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
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.143 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.8984 (tmm160) cc_final: 0.8740 (tmm160)
REVERT: C  444 LYS cc_start: 0.6329 (ttpt) cc_final: 0.6057 (ttpt)
REVERT: E   47 TRP cc_start: 0.8596 (t60) cc_final: 0.8371 (t60)
REVERT: E  230 ARG cc_start: 0.8332 (ptp-170) cc_final: 0.7995 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0862
  time to fit residues: 5.8995
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  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0770
   chunk 13 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0030
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.5350

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.106827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.095729 restraints weight = 12651.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.098124 restraints weight = 7720.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.099773 restraints weight = 5239.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.100914 restraints weight = 3810.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.101757 restraints weight = 2941.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          0.3352

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= 0.122
  Angle     :  0.661   7.013   4533  Z= 0.328
  Chirality :  0.045   0.152    488
  Planarity :  0.004   0.036    585
  Dihedral  :  6.227  58.484    480
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.42), residues: 407
  helix: -1.30 (1.03), residues: 27
  sheet: -0.45 (0.49), residues: 119
  loop : -1.07 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 454 
 TYR   0.010   0.001   TYR C 453 
 PHE   0.015   0.001   PHE C 392 
 TRP   0.020   0.002   TRP E 169 
 HIS   0.002   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3325)
  covalent geometry    : angle       0.65053 ( 4520)
  SS BOND              : bond        0.00425 (    5)
  SS BOND              : angle       2.37542 (   10)
  hydrogen bonds       : bond        0.03708 (   70)
  hydrogen bonds       : angle       6.48847 (  204)
  link_NAG-ASN         : bond        0.00596 (    1)
  link_NAG-ASN         : angle       1.80361 (    3)

*********************** 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  : 0.124 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.8972 (tmm160) cc_final: 0.8771 (tmm160)
REVERT: C  444 LYS cc_start: 0.6255 (ttpt) cc_final: 0.6032 (ttpt)
REVERT: C  465 GLU cc_start: 0.8527 (tp30) cc_final: 0.8265 (tp30)
REVERT: E  230 ARG cc_start: 0.8397 (ptp-170) cc_final: 0.8108 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0738
  time to fit residues: 5.3706
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  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0970
   chunk 1 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** C 505 HIS ** 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 = 0.3762 r_free = 0.3762 target = 0.105947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.095144 restraints weight = 12355.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.097530 restraints weight = 7556.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.099143 restraints weight = 5105.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.100267 restraints weight = 3709.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.101098 restraints weight = 2860.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3331  Z= 0.140
  Angle     :  0.706   8.020   4533  Z= 0.352
  Chirality :  0.046   0.161    488
  Planarity :  0.004   0.036    585
  Dihedral  :  6.339  59.098    480
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.42), residues: 407
  helix: -1.20 (1.05), residues: 27
  sheet: -0.62 (0.46), residues: 132
  loop : -1.12 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 454 
 TYR   0.008   0.001   TYR C 453 
 PHE   0.019   0.002   PHE E  58 
 TRP   0.031   0.003   TRP E 169 
 HIS   0.001   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3325)
  covalent geometry    : angle       0.69575 ( 4520)
  SS BOND              : bond        0.00511 (    5)
  SS BOND              : angle       2.52456 (   10)
  hydrogen bonds       : bond        0.03860 (   70)
  hydrogen bonds       : angle       6.50089 (  204)
  link_NAG-ASN         : bond        0.00606 (    1)
  link_NAG-ASN         : angle       1.83726 (    3)

*********************** 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  : 0.129 
Fit side-chains
REVERT: C  444 LYS cc_start: 0.6302 (ttpt) cc_final: 0.6031 (ttpt)
REVERT: C  465 GLU cc_start: 0.8536 (tp30) cc_final: 0.8255 (tp30)
REVERT: E   89 ASP cc_start: 0.4731 (p0) cc_final: 0.4447 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0898
  time to fit residues: 6.0286
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  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.104997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.093969 restraints weight = 12578.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.096284 restraints weight = 7806.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.097864 restraints weight = 5302.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.099022 restraints weight = 3893.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.099870 restraints weight = 3009.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3331  Z= 0.143
  Angle     :  0.721   8.943   4533  Z= 0.354
  Chirality :  0.046   0.182    488
  Planarity :  0.004   0.037    585
  Dihedral  :  6.317  58.286    480
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.42), residues: 407
  helix: -1.39 (1.23), residues: 20
  sheet: -0.66 (0.47), residues: 128
  loop : -1.07 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 195 
 TYR   0.009   0.001   TYR C 449 
 PHE   0.018   0.001   PHE C 392 
 TRP   0.026   0.003   TRP E 169 
 HIS   0.001   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3325)
  covalent geometry    : angle       0.71020 ( 4520)
  SS BOND              : bond        0.00405 (    5)
  SS BOND              : angle       2.51302 (   10)
  hydrogen bonds       : bond        0.03919 (   70)
  hydrogen bonds       : angle       6.44915 (  204)
  link_NAG-ASN         : bond        0.00610 (    1)
  link_NAG-ASN         : angle       1.94153 (    3)

*********************** 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
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.122 
Fit side-chains
REVERT: C  408 ARG cc_start: 0.9018 (tmm160) cc_final: 0.8758 (tmm160)
REVERT: C  444 LYS cc_start: 0.6327 (ttpt) cc_final: 0.6079 (ttpt)
REVERT: C  465 GLU cc_start: 0.8606 (tp30) cc_final: 0.8287 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0870
  time to fit residues: 5.9570
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  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0170
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 27 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.4618

-------------------------------------------------------------------------------
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 = 0.3787 r_free = 0.3787 target = 0.107322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.096140 restraints weight = 12480.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.098558 restraints weight = 7683.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.100255 restraints weight = 5177.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.101394 restraints weight = 3735.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.102263 restraints weight = 2879.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.4059

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= 0.122
  Angle     :  0.685   7.342   4533  Z= 0.340
  Chirality :  0.045   0.167    488
  Planarity :  0.004   0.039    585
  Dihedral  :  6.195  57.968    480
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.42), residues: 407
  helix: -1.61 (0.97), residues: 27
  sheet: -0.66 (0.46), residues: 129
  loop : -1.08 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 454 
 TYR   0.007   0.001   TYR C 508 
 PHE   0.018   0.001   PHE E  58 
 TRP   0.019   0.002   TRP E 169 
 HIS   0.017   0.006   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3325)
  covalent geometry    : angle       0.67481 ( 4520)
  SS BOND              : bond        0.00437 (    5)
  SS BOND              : angle       2.37466 (   10)
  hydrogen bonds       : bond        0.03693 (   70)
  hydrogen bonds       : angle       6.29383 (  204)
  link_NAG-ASN         : bond        0.00553 (    1)
  link_NAG-ASN         : angle       1.91262 (    3)

*********************** 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
  59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8979 (tmm160) cc_final: 0.8725 (tmm160)
REVERT: C  444 LYS cc_start: 0.6224 (ttpt) cc_final: 0.5961 (ttpt)
REVERT: C  453 TYR cc_start: 0.7145 (p90) cc_final: 0.6929 (p90)
REVERT: C  465 GLU cc_start: 0.8583 (tp30) cc_final: 0.8337 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0750
  time to fit residues: 5.3107
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  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 38 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0770
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0170
   chunk 0 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.4376

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.107924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.096671 restraints weight = 11907.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.099099 restraints weight = 7309.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.100719 restraints weight = 4939.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.101919 restraints weight = 3610.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.102765 restraints weight = 2766.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.4106

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= 0.119
  Angle     :  0.674   7.530   4533  Z= 0.334
  Chirality :  0.046   0.169    488
  Planarity :  0.004   0.038    585
  Dihedral  :  6.075  57.787    480
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.42), residues: 407
  helix: -1.25 (1.22), residues: 20
  sheet: -0.70 (0.46), residues: 128
  loop : -1.00 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 454 
 TYR   0.007   0.001   TYR C 508 
 PHE   0.013   0.001   PHE C 392 
 TRP   0.020   0.002   TRP E 169 
 HIS   0.010   0.003   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3325)
  covalent geometry    : angle       0.66453 ( 4520)
  SS BOND              : bond        0.00426 (    5)
  SS BOND              : angle       2.29529 (   10)
  hydrogen bonds       : bond        0.03541 (   70)
  hydrogen bonds       : angle       6.21651 (  204)
  link_NAG-ASN         : bond        0.00543 (    1)
  link_NAG-ASN         : angle       1.89876 (    3)

*********************** 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
  58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: C  444 LYS cc_start: 0.6306 (ttpt) cc_final: 0.6070 (ttpt)
REVERT: C  465 GLU cc_start: 0.8598 (tp30) cc_final: 0.8384 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0696
  time to fit residues: 4.7521
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  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0040
   overall best weight:    0.5192

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.106897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.096025 restraints weight = 12505.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.098352 restraints weight = 7760.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.099935 restraints weight = 5297.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.101079 restraints weight = 3880.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.101912 restraints weight = 2999.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.4305

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     :  0.685   7.381   4533  Z= 0.342
  Chirality :  0.046   0.172    488
  Planarity :  0.004   0.038    585
  Dihedral  :  6.154  58.073    480
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.42), residues: 407
  helix:  0.44 (1.60), residues: 14
  sheet: -0.73 (0.46), residues: 128
  loop : -1.11 (0.39), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 454 
 TYR   0.007   0.001   TYR E 183 
 PHE   0.016   0.001   PHE E  58 
 TRP   0.020   0.002   TRP E 169 
 HIS   0.007   0.003   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3325)
  covalent geometry    : angle       0.67574 ( 4520)
  SS BOND              : bond        0.00417 (    5)
  SS BOND              : angle       2.30410 (   10)
  hydrogen bonds       : bond        0.03700 (   70)
  hydrogen bonds       : angle       6.29770 (  204)
  link_NAG-ASN         : bond        0.00559 (    1)
  link_NAG-ASN         : angle       1.98643 (    3)

********************** 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
  56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: C  444 LYS cc_start: 0.6312 (ttpt) cc_final: 0.6091 (ttpt)
REVERT: C  465 GLU cc_start: 0.8581 (tp30) cc_final: 0.8333 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0747
  time to fit residues: 4.9520
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  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0670
   overall best weight:    0.5718

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.106242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.094849 restraints weight = 12136.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.097384 restraints weight = 7194.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.099135 restraints weight = 4794.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.100377 restraints weight = 3467.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.101215 restraints weight = 2645.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.4314

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= 0.131
  Angle     :  0.690   7.352   4533  Z= 0.344
  Chirality :  0.046   0.179    488
  Planarity :  0.004   0.038    585
  Dihedral  :  6.174  57.731    480
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.42), residues: 407
  helix: -1.31 (0.99), residues: 27
  sheet: -0.72 (0.47), residues: 128
  loop : -1.03 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 408 
 TYR   0.008   0.001   TYR C 453 
 PHE   0.016   0.001   PHE C 392 
 TRP   0.017   0.002   TRP E  47 
 HIS   0.009   0.003   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3325)
  covalent geometry    : angle       0.67768 ( 4520)
  SS BOND              : bond        0.00382 (    5)
  SS BOND              : angle       2.65630 (   10)
  hydrogen bonds       : bond        0.03646 (   70)
  hydrogen bonds       : angle       6.51803 (  204)
  link_NAG-ASN         : bond        0.00563 (    1)
  link_NAG-ASN         : angle       2.00815 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 862.43 seconds
wall clock time: 15 minutes 33.26 seconds (933.26 seconds total)