Starting phenix.real_space_refine
on Tue Mar  3 13:06:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ey4_31377/03_2026/7ey4_31377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ey4_31377/03_2026/7ey4_31377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ey4_31377/03_2026/7ey4_31377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ey4_31377/03_2026/7ey4_31377.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ey4_31377/03_2026/7ey4_31377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ey4_31377/03_2026/7ey4_31377.map"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
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      17      5.16       5
     C    3000      2.51       5
     N     772      2.21       5
     O     894      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4683
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 985
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 126}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1465
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 9, 'TRANS': 173}
    Chain: "N"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1359
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 8, 'TRANS': 156}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.18, per 1000 atoms: 0.25
  Number of scatterers: 4683
  At special positions: 0
  Unit cell: (62.13, 80.66, 110.09, 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      17     16.00
     O     894      8.00
     N     772      7.00
     C    3000      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 131 " - pdb=" SG  CYS N 166 " distance=2.05

  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
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
    NAG-ASN
      " NAG A   1 " - " ASN N 165 "
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 217.4 milliseconds
  

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1072

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 11 sheets defined
      7.2% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.648A  pdb=" N   ASP H  31 " --> pdb=" O   ARG H  28 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'R' and resid 338 through 343
    Processing helix  chain 'R' and resid 349 through 353
    Processing helix  chain 'R' and resid 365 through 370
    Processing helix  chain 'R' and resid 383 through 387
      removed outlier: 3.577A  pdb=" N   LEU R 387 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 405 through 410
      removed outlier: 3.653A  pdb=" N   ARG R 408 " --> pdb=" O   ASP R 405 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 417 through 422
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.923A  pdb=" N   GLU L  70 " --> pdb=" O   PHE L  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 7.193A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL L  85 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.513A  pdb=" N   SER H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASP H  73 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 47
      removed outlier: 4.277A  pdb=" N   TYR H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASN H  35 " --> pdb=" O   ALA H  97 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 117 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 49 through 50
      removed outlier: 3.668A  pdb=" N   TYR H  50 " --> pdb=" O   TYR H  59 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'R' and resid 356 through 358
      removed outlier: 3.687A  pdb=" N   ILE R 402 " --> pdb=" O   TYR R 508 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLY R 431 " --> pdb=" O   TYR R 380 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   TYR R 380 " --> pdb=" O   GLY R 431 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   VAL R 433 " --> pdb=" O   LYS R 378 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS R 378 " --> pdb=" O   VAL R 433 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'R' and resid 473 through 474
    Processing sheet with id=AB1, first strand: chain 'N' and resid 50 through 55
      removed outlier: 3.774A  pdb=" N   ASP N  53 " --> pdb=" O   ARG N 273 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ASP N 287 " --> pdb=" O   LYS N 278 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 63 through 64
  WARNING: can't find start of bonding for strands!
    previous: chain 'N' and resid 63 through 64
    current: chain 'N' and resid 116 through 121
      removed outlier: 4.174A  pdb=" N   ASN N 164 " --> pdb=" O   GLU N 132 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'N' and resid 163 through 164
    current: chain 'N' and resid 200 through 205
      removed outlier: 5.953A  pdb=" N   SER N 205 " --> pdb=" O   PRO N 225 " (cutoff:3.500A)

    103 hydrogen bonds defined for protein.
    252 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: 0.69

  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:
        1.22 -     1.35: 1473
        1.35 -     1.48: 1418
        1.48 -     1.61: 1891
        1.61 -     1.74: 0
        1.74 -     1.88: 21
  Bond restraints: 4803
  Sorted by residual:
  bond pdb=" CA  SER H 107 "
       pdb=" CB  SER H 107 "
    ideal  model  delta    sigma   weight residual
    1.532  1.464  0.067 1.82e-02 3.02e+03 1.37e+01
  bond pdb=" N   CYS N 166 "
       pdb=" CA  CYS N 166 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.58e+00
  bond pdb=" N   PHE N 168 "
       pdb=" CA  PHE N 168 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.033 1.22e-02 6.72e+03 7.54e+00
  bond pdb=" CA  SER H 104 "
       pdb=" CB  SER H 104 "
    ideal  model  delta    sigma   weight residual
    1.524  1.491  0.033 1.22e-02 6.72e+03 7.34e+00
  bond pdb=" N   ASP H 105 "
       pdb=" CA  ASP H 105 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.036 1.34e-02 5.57e+03 7.04e+00
  ... (remaining 4798 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 6374
        2.63 -     5.25: 127
        5.25 -     7.88: 15
        7.88 -    10.50: 1
       10.50 -    13.13: 2
  Bond angle restraints: 6519
  Sorted by residual:
  angle pdb=" N   VAL L  29 "
        pdb=" CA  VAL L  29 "
        pdb=" C   VAL L  29 "
      ideal   model   delta    sigma   weight residual
     111.90  107.22    4.68 8.10e-01 1.52e+00 3.34e+01
  angle pdb=" CA  CYS R 379 "
        pdb=" CB  CYS R 379 "
        pdb=" SG  CYS R 379 "
      ideal   model   delta    sigma   weight residual
     114.40  127.53  -13.13 2.30e+00 1.89e-01 3.26e+01
  angle pdb=" CA  CYS R 432 "
        pdb=" CB  CYS R 432 "
        pdb=" SG  CYS R 432 "
      ideal   model   delta    sigma   weight residual
     114.40  127.18  -12.78 2.30e+00 1.89e-01 3.09e+01
  angle pdb=" N   CYS R 379 "
        pdb=" CA  CYS R 379 "
        pdb=" C   CYS R 379 "
      ideal   model   delta    sigma   weight residual
     108.38  114.13   -5.75 1.35e+00 5.49e-01 1.82e+01
  angle pdb=" N   CYS R 432 "
        pdb=" CA  CYS R 432 "
        pdb=" C   CYS R 432 "
      ideal   model   delta    sigma   weight residual
     108.60  114.65   -6.05 1.46e+00 4.69e-01 1.71e+01
  ... (remaining 6514 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.25: 2582
       21.25 -    42.51: 184
       42.51 -    63.76: 27
       63.76 -    85.01: 13
       85.01 -   106.26: 12
  Dihedral angle restraints: 2818
    sinusoidal: 1129
      harmonic: 1689
  Sorted by residual:
  dihedral pdb=" CA  SER L   7 "
           pdb=" C   SER L   7 "
           pdb=" N   PRO L   8 "
           pdb=" CA  PRO L   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.41   47.59     0      5.00e+00 4.00e-02 9.06e+01
  dihedral pdb=" CB  CYS R 379 "
           pdb=" SG  CYS R 379 "
           pdb=" SG  CYS R 432 "
           pdb=" CB  CYS R 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -10.28  -75.72     1      1.00e+01 1.00e-02 7.23e+01
  dihedral pdb=" CA  CYS R 379 "
           pdb=" C   CYS R 379 "
           pdb=" N   TYR R 380 "
           pdb=" CA  TYR R 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.32  -39.68     0      5.00e+00 4.00e-02 6.30e+01
  ... (remaining 2815 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 624
       0.078 -    0.156: 70
       0.156 -    0.233: 4
       0.233 -    0.311: 2
       0.311 -    0.389: 1
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" C1  BMA A   3 "
            pdb=" O4  NAG A   2 "
            pdb=" C2  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-02 2.50e+03 3.79e+02
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.37   -0.03 2.00e-02 2.50e+03 2.58e+00
  chirality pdb=" CA  CYS R 432 "
            pdb=" N   CYS R 432 "
            pdb=" C   CYS R 432 "
            pdb=" CB  CYS R 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 698 not shown)

  Planarity restraints: 836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "   -0.322 2.00e-02 2.50e+03   2.72e-01 9.26e+02
        pdb=" C7  NAG A   1 "    0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "   -0.188 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "    0.471 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   2 "   -0.293 2.00e-02 2.50e+03   2.52e-01 7.94e+02
        pdb=" C7  NAG A   2 "    0.063 2.00e-02 2.50e+03
        pdb=" C8  NAG A   2 "    0.007 2.00e-02 2.50e+03
        pdb=" N2  NAG A   2 "    0.430 2.00e-02 2.50e+03
        pdb=" O7  NAG A   2 "   -0.208 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L   7 "    0.042 5.00e-02 4.00e+02   6.38e-02 6.52e+00
        pdb=" N   PRO L   8 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "    0.035 5.00e-02 4.00e+02
  ... (remaining 833 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 180
        2.70 -     3.25: 4472
        3.25 -     3.80: 6731
        3.80 -     4.35: 8835
        4.35 -     4.90: 15297
  Nonbonded interactions: 35515
  Sorted by model distance:
  nonbonded pdb=" OH  TYR N  37 "
            pdb=" O   LEU N  54 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" OD1 ASP N  40 "
            pdb=" OH  TYR N 204 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OH  TYR N  91 "
            pdb=" OE1 GLU N 191 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" NH2 ARG H  98 "
            pdb=" OD2 ASP H 117 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" NH2 ARG L  31 "
            pdb=" OE1 GLU R 340 "
     model   vdw
     2.241 3.120
  ... (remaining 35510 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.110
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.880
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
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      :  0.007   0.068   4812  Z= 0.328
  Angle     :  0.941  13.127   6540  Z= 0.524
  Chirality :  0.053   0.389    701
  Planarity :  0.014   0.272    835
  Dihedral  : 16.811 106.261   1728
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 13.50 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.60 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.34), residues: 563
  helix: -3.57 (0.84), residues: 20
  sheet: -0.83 (0.39), residues: 181
  loop : -2.14 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG N  44 
 TYR   0.024   0.002   TYR H 110 
 PHE   0.028   0.002   PHE H  56 
 TRP   0.016   0.002   TRP R 436 
 HIS   0.001   0.001   HIS N  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00695 ( 4803)
  covalent geometry    : angle       0.90135 ( 6519)
  SS BOND              : bond        0.00982 (    6)
  SS BOND              : angle       4.82403 (   12)
  hydrogen bonds       : bond        0.29872 (  103)
  hydrogen bonds       : angle      10.92957 (  252)
  link_BETA1-4         : bond        0.00559 (    2)
  link_BETA1-4         : angle       3.11479 (    6)
  link_NAG-ASN         : bond        0.02273 (    1)
  link_NAG-ASN         : angle       7.17095 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.167 
Fit side-chains
REVERT: H   74 ASP cc_start: 0.8334 (m-30) cc_final: 0.7991 (m-30)
REVERT: N   54 LEU cc_start: 0.7149 (mp) cc_final: 0.6142 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1044
  time to fit residues: 15.7675
Evaluate side-chains
  98 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
H 109 ASN
N 164 ASN
N 282 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.144692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.115303 restraints weight = 6599.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.116209 restraints weight = 6052.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.117327 restraints weight = 4832.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.117826 restraints weight = 4129.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.118315 restraints weight = 3868.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4812  Z= 0.205
  Angle     :  0.783   8.742   6540  Z= 0.406
  Chirality :  0.050   0.322    701
  Planarity :  0.005   0.059    835
  Dihedral  : 12.357  84.376    708
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.59 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.40 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.34), residues: 563
  helix: -3.46 (0.93), residues: 20
  sheet: -0.27 (0.40), residues: 182
  loop : -2.11 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N 237 
 TYR   0.014   0.002   TYR R 369 
 PHE   0.017   0.002   PHE H  56 
 TRP   0.017   0.002   TRP R 436 
 HIS   0.001   0.000   HIS N  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 4803)
  covalent geometry    : angle       0.76580 ( 6519)
  SS BOND              : bond        0.00675 (    6)
  SS BOND              : angle       3.22976 (   12)
  hydrogen bonds       : bond        0.04381 (  103)
  hydrogen bonds       : angle       7.32575 (  252)
  link_BETA1-4         : bond        0.00561 (    2)
  link_BETA1-4         : angle       3.00762 (    6)
  link_NAG-ASN         : bond        0.00404 (    1)
  link_NAG-ASN         : angle       0.93990 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.159 
Fit side-chains
REVERT: H   74 ASP cc_start: 0.8393 (m-30) cc_final: 0.8050 (m-30)
REVERT: R  378 LYS cc_start: 0.7791 (ptpt) cc_final: 0.7577 (ptpp)
REVERT: R  414 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7297 (mm-40)
  outliers start: 7
  outliers final: 5
  residues processed: 108
  average time/residue: 0.0904
  time to fit residues: 11.9377
Evaluate side-chains
  94 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain N residue   51 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0070
   chunk 52 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
N  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.146972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.117914 restraints weight = 6556.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.119871 restraints weight = 5446.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.120750 restraints weight = 4534.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.121190 restraints weight = 3898.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.121565 restraints weight = 3703.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4812  Z= 0.154
  Angle     :  0.700   8.400   6540  Z= 0.360
  Chirality :  0.047   0.240    701
  Planarity :  0.005   0.086    835
  Dihedral  : 10.320  73.973    708
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.24 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.00 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.34), residues: 563
  helix: -3.33 (0.97), residues: 20
  sheet: -0.26 (0.39), residues: 189
  loop : -2.03 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  54 
 TYR   0.014   0.001   TYR R 369 
 PHE   0.015   0.001   PHE N  32 
 TRP   0.014   0.002   TRP R 436 
 HIS   0.001   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 4803)
  covalent geometry    : angle       0.68221 ( 6519)
  SS BOND              : bond        0.00526 (    6)
  SS BOND              : angle       3.13444 (   12)
  hydrogen bonds       : bond        0.03881 (  103)
  hydrogen bonds       : angle       6.56955 (  252)
  link_BETA1-4         : bond        0.01083 (    2)
  link_BETA1-4         : angle       2.73164 (    6)
  link_NAG-ASN         : bond        0.00135 (    1)
  link_NAG-ASN         : angle       1.22859 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: H   74 ASP cc_start: 0.8405 (m-30) cc_final: 0.8038 (m-30)
REVERT: N  113 LYS cc_start: 0.7552 (mtmm) cc_final: 0.7251 (mtmm)
  outliers start: 15
  outliers final: 8
  residues processed: 109
  average time/residue: 0.0923
  time to fit residues: 12.1472
Evaluate side-chains
  95 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 55 optimal weight:    0.1980
   chunk 43 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 52 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9990
   chunk 41 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
N  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.118601 restraints weight = 6527.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.120612 restraints weight = 5103.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.122093 restraints weight = 4312.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.123117 restraints weight = 3826.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.123581 restraints weight = 3516.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   4812  Z= 0.140
  Angle     :  0.717   9.818   6540  Z= 0.362
  Chirality :  0.045   0.250    701
  Planarity :  0.005   0.089    835
  Dihedral  :  8.854  63.122    708
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 15.60 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.35), residues: 563
  helix: -3.06 (1.01), residues: 20
  sheet: -0.11 (0.39), residues: 186
  loop : -1.88 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  54 
 TYR   0.011   0.001   TYR H 110 
 PHE   0.016   0.001   PHE N 168 
 TRP   0.013   0.001   TRP R 436 
 HIS   0.001   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 4803)
  covalent geometry    : angle       0.69139 ( 6519)
  SS BOND              : bond        0.00593 (    6)
  SS BOND              : angle       3.88857 (   12)
  hydrogen bonds       : bond        0.03504 (  103)
  hydrogen bonds       : angle       6.20685 (  252)
  link_BETA1-4         : bond        0.00988 (    2)
  link_BETA1-4         : angle       2.82796 (    6)
  link_NAG-ASN         : bond        0.00098 (    1)
  link_NAG-ASN         : angle       2.20492 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.172 
Fit side-chains
REVERT: L   93 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7506 (m-40)
REVERT: H   74 ASP cc_start: 0.8404 (m-30) cc_final: 0.8091 (m-30)
REVERT: H  114 ASP cc_start: 0.8890 (t0) cc_final: 0.8634 (t0)
REVERT: N  113 LYS cc_start: 0.7587 (mtmm) cc_final: 0.7329 (mtmm)
  outliers start: 21
  outliers final: 12
  residues processed: 116
  average time/residue: 0.0762
  time to fit residues: 11.0244
Evaluate side-chains
  100 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue   93 ASN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   43 PHE
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0570
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.8300

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

Flipped N/Q/H residues before XYZ refinement:
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.144035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.113518 restraints weight = 6640.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.115542 restraints weight = 5205.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.117010 restraints weight = 4410.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.117879 restraints weight = 3932.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.118639 restraints weight = 3636.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   4812  Z= 0.211
  Angle     :  0.758  10.595   6540  Z= 0.386
  Chirality :  0.047   0.232    701
  Planarity :  0.005   0.081    835
  Dihedral  :  8.024  51.230    708
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.12 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 17.60 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.35), residues: 563
  helix: -3.05 (0.95), residues: 20
  sheet:  0.03 (0.39), residues: 195
  loop : -2.04 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  54 
 TYR   0.014   0.001   TYR H 110 
 PHE   0.023   0.002   PHE H  56 
 TRP   0.015   0.002   TRP R 436 
 HIS   0.001   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 4803)
  covalent geometry    : angle       0.72922 ( 6519)
  SS BOND              : bond        0.00782 (    6)
  SS BOND              : angle       4.21842 (   12)
  hydrogen bonds       : bond        0.03843 (  103)
  hydrogen bonds       : angle       6.08539 (  252)
  link_BETA1-4         : bond        0.01158 (    2)
  link_BETA1-4         : angle       3.13991 (    6)
  link_NAG-ASN         : bond        0.00174 (    1)
  link_NAG-ASN         : angle       2.29977 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.155 
Fit side-chains
REVERT: L   24 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7992 (ttp80)
REVERT: H   74 ASP cc_start: 0.8398 (m-30) cc_final: 0.8107 (m-30)
REVERT: H  114 ASP cc_start: 0.9097 (t0) cc_final: 0.8855 (t0)
REVERT: N   52 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7626 (pp30)
  outliers start: 23
  outliers final: 15
  residues processed: 112
  average time/residue: 0.0840
  time to fit residues: 11.5662
Evaluate side-chains
  107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 47 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 28 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.142588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.111418 restraints weight = 6579.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.113616 restraints weight = 5040.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.115028 restraints weight = 4210.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.116103 restraints weight = 3724.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.117133 restraints weight = 3388.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   4812  Z= 0.169
  Angle     :  0.739  13.108   6540  Z= 0.374
  Chirality :  0.046   0.207    701
  Planarity :  0.005   0.093    835
  Dihedral  :  7.055  39.554    708
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 18.40 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.35), residues: 563
  helix: -2.83 (1.01), residues: 20
  sheet:  0.05 (0.39), residues: 190
  loop : -1.94 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  54 
 TYR   0.011   0.001   TYR H 110 
 PHE   0.020   0.002   PHE N  43 
 TRP   0.016   0.001   TRP R 436 
 HIS   0.001   0.000   HIS N  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 4803)
  covalent geometry    : angle       0.71242 ( 6519)
  SS BOND              : bond        0.00658 (    6)
  SS BOND              : angle       3.87802 (   12)
  hydrogen bonds       : bond        0.03615 (  103)
  hydrogen bonds       : angle       6.02855 (  252)
  link_BETA1-4         : bond        0.01289 (    2)
  link_BETA1-4         : angle       3.32208 (    6)
  link_NAG-ASN         : bond        0.00052 (    1)
  link_NAG-ASN         : angle       2.37575 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.167 
Fit side-chains
REVERT: H  114 ASP cc_start: 0.9069 (t0) cc_final: 0.8839 (t0)
REVERT: N   52 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7635 (pp30)
  outliers start: 21
  outliers final: 15
  residues processed: 109
  average time/residue: 0.0812
  time to fit residues: 10.9546
Evaluate side-chains
  105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0770
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
R 360 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.142965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.111775 restraints weight = 6493.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.113781 restraints weight = 5005.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.115381 restraints weight = 4220.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.116499 restraints weight = 3736.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.117144 restraints weight = 3427.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   4812  Z= 0.158
  Angle     :  0.739  15.126   6540  Z= 0.375
  Chirality :  0.046   0.165    701
  Planarity :  0.005   0.089    835
  Dihedral  :  6.238  38.925    708
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.00 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.35), residues: 563
  helix: -2.71 (1.05), residues: 20
  sheet:  0.14 (0.39), residues: 192
  loop : -1.87 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  54 
 TYR   0.012   0.001   TYR L  49 
 PHE   0.028   0.002   PHE N  43 
 TRP   0.016   0.001   TRP R 436 
 HIS   0.001   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 4803)
  covalent geometry    : angle       0.71304 ( 6519)
  SS BOND              : bond        0.00677 (    6)
  SS BOND              : angle       3.66612 (   12)
  hydrogen bonds       : bond        0.03512 (  103)
  hydrogen bonds       : angle       5.90432 (  252)
  link_BETA1-4         : bond        0.01527 (    2)
  link_BETA1-4         : angle       3.45732 (    6)
  link_NAG-ASN         : bond        0.00051 (    1)
  link_NAG-ASN         : angle       2.64746 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.184 
Fit side-chains
REVERT: N   52 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7696 (pp30)
REVERT: N  237 ARG cc_start: 0.8619 (mtp-110) cc_final: 0.8237 (mtm110)
  outliers start: 19
  outliers final: 18
  residues processed: 104
  average time/residue: 0.0972
  time to fit residues: 12.2304
Evaluate side-chains
  104 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  113 ASP
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  166 CYS
Chi-restraints excluded: chain N residue  240 THR
Chi-restraints excluded: chain N residue  276 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0040
   chunk 55 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.3770

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.144571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.113145 restraints weight = 6548.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.115143 restraints weight = 5060.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.116895 restraints weight = 4257.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.118061 restraints weight = 3747.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.118723 restraints weight = 3421.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.4010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4812  Z= 0.140
  Angle     :  0.725  16.051   6540  Z= 0.368
  Chirality :  0.045   0.175    701
  Planarity :  0.005   0.082    835
  Dihedral  :  5.676  35.992    708
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 21.20 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.35), residues: 563
  helix: -2.49 (1.11), residues: 20
  sheet:  0.35 (0.39), residues: 186
  loop : -1.82 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  54 
 TYR   0.010   0.001   TYR H 110 
 PHE   0.036   0.001   PHE N  43 
 TRP   0.015   0.001   TRP R 436 
 HIS   0.001   0.000   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4803)
  covalent geometry    : angle       0.70326 ( 6519)
  SS BOND              : bond        0.00669 (    6)
  SS BOND              : angle       3.30776 (   12)
  hydrogen bonds       : bond        0.03290 (  103)
  hydrogen bonds       : angle       5.85091 (  252)
  link_BETA1-4         : bond        0.01486 (    2)
  link_BETA1-4         : angle       3.26749 (    6)
  link_NAG-ASN         : bond        0.00039 (    1)
  link_NAG-ASN         : angle       2.73608 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.202 
Fit side-chains
REVERT: L   74 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8366 (p)
REVERT: H   87 ARG cc_start: 0.7706 (ptp-170) cc_final: 0.7419 (ptp-170)
REVERT: H  114 ASP cc_start: 0.8731 (t0) cc_final: 0.8452 (t0)
REVERT: R  493 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7927 (mm-40)
REVERT: N   44 ARG cc_start: 0.5545 (ttm170) cc_final: 0.4610 (mpt180)
REVERT: N   52 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7739 (pp30)
REVERT: N  237 ARG cc_start: 0.8585 (mtp-110) cc_final: 0.8168 (mtm110)
  outliers start: 20
  outliers final: 15
  residues processed: 105
  average time/residue: 0.1013
  time to fit residues: 12.8692
Evaluate side-chains
  108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  105 ILE
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0770
   chunk 28 optimal weight:    0.3980
   chunk 53 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0170
   chunk 29 optimal weight:    0.0870
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.1354

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.148601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.117988 restraints weight = 6466.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.120021 restraints weight = 5101.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.121305 restraints weight = 4340.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.122539 restraints weight = 3893.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.123121 restraints weight = 3579.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.4246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4812  Z= 0.122
  Angle     :  0.696  14.732   6540  Z= 0.354
  Chirality :  0.044   0.229    701
  Planarity :  0.005   0.095    835
  Dihedral  :  5.251  37.020    708
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 22.60 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.35), residues: 563
  helix: -2.48 (1.12), residues: 20
  sheet:  0.46 (0.40), residues: 186
  loop : -1.53 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  54 
 TYR   0.009   0.001   TYR L  49 
 PHE   0.029   0.001   PHE N  43 
 TRP   0.023   0.001   TRP L  97 
 HIS   0.001   0.000   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4803)
  covalent geometry    : angle       0.67700 ( 6519)
  SS BOND              : bond        0.00815 (    6)
  SS BOND              : angle       2.87461 (   12)
  hydrogen bonds       : bond        0.02940 (  103)
  hydrogen bonds       : angle       5.67550 (  252)
  link_BETA1-4         : bond        0.01516 (    2)
  link_BETA1-4         : angle       3.05272 (    6)
  link_NAG-ASN         : bond        0.00290 (    1)
  link_NAG-ASN         : angle       2.81946 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.136 
Fit side-chains
REVERT: L   74 THR cc_start: 0.8642 (m) cc_final: 0.8383 (p)
REVERT: R  493 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7863 (mm-40)
REVERT: N   44 ARG cc_start: 0.5383 (ttm170) cc_final: 0.4571 (mpt180)
REVERT: N   52 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7709 (pp30)
REVERT: N  237 ARG cc_start: 0.8521 (mtp-110) cc_final: 0.8102 (mtm110)
  outliers start: 15
  outliers final: 13
  residues processed: 103
  average time/residue: 0.0958
  time to fit residues: 12.0048
Evaluate side-chains
  105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0470
   chunk 12 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 = 0.3676 r_free = 0.3676 target = 0.144280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.113773 restraints weight = 6586.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.115029 restraints weight = 6047.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115824 restraints weight = 4889.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.116211 restraints weight = 4457.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.116459 restraints weight = 4227.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.4219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4812  Z= 0.170
  Angle     :  0.740  14.645   6540  Z= 0.377
  Chirality :  0.046   0.245    701
  Planarity :  0.005   0.099    835
  Dihedral  :  5.434  36.118    708
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 23.60 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.35), residues: 563
  helix: -2.47 (1.11), residues: 20
  sheet:  0.21 (0.39), residues: 191
  loop : -1.73 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG L  54 
 TYR   0.013   0.001   TYR H 110 
 PHE   0.029   0.002   PHE N  43 
 TRP   0.019   0.002   TRP L  97 
 HIS   0.001   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 4803)
  covalent geometry    : angle       0.71922 ( 6519)
  SS BOND              : bond        0.00854 (    6)
  SS BOND              : angle       3.37950 (   12)
  hydrogen bonds       : bond        0.03103 (  103)
  hydrogen bonds       : angle       5.72686 (  252)
  link_BETA1-4         : bond        0.01603 (    2)
  link_BETA1-4         : angle       2.98509 (    6)
  link_NAG-ASN         : bond        0.00179 (    1)
  link_NAG-ASN         : angle       2.64537 (    3)

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

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

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1126 Ramachandran restraints generated.
    563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.175 
Fit side-chains
REVERT: L   74 THR cc_start: 0.8677 (m) cc_final: 0.8401 (p)
REVERT: R  493 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7963 (mm-40)
REVERT: N   44 ARG cc_start: 0.6038 (ttm170) cc_final: 0.4693 (mpt180)
REVERT: N   52 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7794 (pp30)
REVERT: N  237 ARG cc_start: 0.8622 (mtp-110) cc_final: 0.8230 (mtm110)
  outliers start: 13
  outliers final: 13
  residues processed: 103
  average time/residue: 0.1023
  time to fit residues: 12.7389
Evaluate side-chains
  107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  379 CYS
Chi-restraints excluded: chain R residue  380 TYR
Chi-restraints excluded: chain N residue   33 THR
Chi-restraints excluded: chain N residue   62 VAL
Chi-restraints excluded: chain N residue   83 VAL
Chi-restraints excluded: chain N residue  130 VAL
Chi-restraints excluded: chain N residue  240 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 50 optimal weight:    0.2980
   chunk 35 optimal weight:    0.5980
   chunk 31 optimal weight:    0.1980
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0970
   chunk 36 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 11 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.1778

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

Flipped N/Q/H residues before XYZ refinement:
R 334 ASN
R 360 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.148223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.117556 restraints weight = 6524.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.119411 restraints weight = 5128.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.120935 restraints weight = 4359.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.121745 restraints weight = 3883.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.122761 restraints weight = 3600.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.4385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4812  Z= 0.123
  Angle     :  0.692  13.027   6540  Z= 0.353
  Chirality :  0.044   0.230    701
  Planarity :  0.005   0.099    835
  Dihedral  :  5.173  34.744    708
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.20 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.36), residues: 563
  helix: -3.01 (0.88), residues: 26
  sheet:  0.50 (0.40), residues: 186
  loop : -1.50 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  54 
 TYR   0.008   0.001   TYR H 110 
 PHE   0.029   0.001   PHE N  43 
 TRP   0.025   0.002   TRP L  97 
 HIS   0.001   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4803)
  covalent geometry    : angle       0.67581 ( 6519)
  SS BOND              : bond        0.00466 (    6)
  SS BOND              : angle       2.84658 (   12)
  hydrogen bonds       : bond        0.02884 (  103)
  hydrogen bonds       : angle       5.60911 (  252)
  link_BETA1-4         : bond        0.01497 (    2)
  link_BETA1-4         : angle       2.76402 (    6)
  link_NAG-ASN         : bond        0.00078 (    1)
  link_NAG-ASN         : angle       2.24970 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1003.02 seconds
wall clock time: 17 minutes 54.75 seconds (1074.75 seconds total)