Starting phenix.real_space_refine
on Tue Mar  3 13:20:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7upx_26677/03_2026/7upx_26677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7upx_26677/03_2026/7upx_26677.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7upx_26677/03_2026/7upx_26677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7upx_26677/03_2026/7upx_26677.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7upx_26677/03_2026/7upx_26677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7upx_26677/03_2026/7upx_26677.map"
  }
  resolution = 3.2
  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=   0.018
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      20      5.16       5
     C    3112      2.51       5
     N     821      2.21       5
     O     977      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4930
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1569
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 11, 'TRANS': 186}
    Chain: "H"
      Number of atoms: 1701
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1701
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 213}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "L"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1622
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 200}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 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: 1.17, per 1000 atoms: 0.24
  Number of scatterers: 4930
  At special positions: 0
  Unit cell: (96.28, 82.17, 110.39, 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      20     16.00
     O     977      8.00
     N     821      7.00
     C    3112      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    BETA1-6
      " NAG B   1 " - " FUC B   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 296.3 milliseconds
  

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1172

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 13 sheets defined
      12.1% alpha, 35.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.072A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
      removed outlier: 3.579A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 4.232A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ALA A 411 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 73 through 75
      No H-bonds generated for 'chain 'H' and resid 73 through 75'
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'H' and resid 156 through 158
      No H-bonds generated for 'chain 'H' and resid 156 through 158'
    Processing helix  chain 'H' and resid 187 through 191
      removed outlier: 3.990A  pdb=" N   GLY H 190 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 201 through 204
    Processing helix  chain 'L' and resid 121 through 127
    Processing helix  chain 'L' and resid 183 through 188
      removed outlier: 3.652A  pdb=" N   GLU L 187 " --> pdb=" O   LYS L 183 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LYS L 188 " --> pdb=" O   ALA L 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 183 through 188'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.513A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.877A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.524A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 120 through 124
      removed outlier: 5.965A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124
      removed outlier: 5.965A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 151 through 154
      removed outlier: 4.205A  pdb=" N   TYR H 194 " --> pdb=" O   VAL H 211 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6
      removed outlier: 4.317A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER L  67 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.264A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118
      removed outlier: 6.411A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 153 through 154

    188 hydrogen bonds defined for protein.
    456 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: 0.77

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 819
        1.30 -     1.43: 1420
        1.43 -     1.56: 2788
        1.56 -     1.69: 1
        1.69 -     1.82: 23
  Bond restraints: 5051
  Sorted by residual:
  bond pdb=" C   TYR H 145 "
       pdb=" O   TYR H 145 "
    ideal  model  delta    sigma   weight residual
    1.235  1.174  0.061 1.22e-02 6.72e+03 2.49e+01
  bond pdb=" C1  FUC B   3 "
       pdb=" O5  FUC B   3 "
    ideal  model  delta    sigma   weight residual
    1.400  1.481 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" CA  ARG A 466 "
       pdb=" C   ARG A 466 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 1.20e-02 6.94e+03 1.45e+01
  bond pdb=" C6  NAG B   1 "
       pdb=" O6  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.408  1.478 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" C5  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.482 -0.069 2.00e-02 2.50e+03 1.20e+01
  ... (remaining 5046 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.70: 5882
        2.70 -     5.39: 936
        5.39 -     8.09: 49
        8.09 -    10.78: 7
       10.78 -    13.48: 4
  Bond angle restraints: 6878
  Sorted by residual:
  angle pdb=" C   GLU H 148 "
        pdb=" N   PRO H 149 "
        pdb=" CA  PRO H 149 "
      ideal   model   delta    sigma   weight residual
     119.84  133.01  -13.17 1.25e+00 6.40e-01 1.11e+02
  angle pdb=" N   PHE H 146 "
        pdb=" CA  PHE H 146 "
        pdb=" C   PHE H 146 "
      ideal   model   delta    sigma   weight residual
     109.81  123.29  -13.48 2.21e+00 2.05e-01 3.72e+01
  angle pdb=" CA  PHE H 100G"
        pdb=" CB  PHE H 100G"
        pdb=" CG  PHE H 100G"
      ideal   model   delta    sigma   weight residual
     113.80  119.88   -6.08 1.00e+00 1.00e+00 3.70e+01
  angle pdb=" C   ARG H  82B"
        pdb=" N   LEU H  82C"
        pdb=" CA  LEU H  82C"
      ideal   model   delta    sigma   weight residual
     121.05  129.71   -8.66 1.43e+00 4.89e-01 3.67e+01
  angle pdb=" CA  ASN A 422 "
        pdb=" CB  ASN A 422 "
        pdb=" CG  ASN A 422 "
      ideal   model   delta    sigma   weight residual
     112.60  118.47   -5.87 1.00e+00 1.00e+00 3.45e+01
  ... (remaining 6873 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.86: 2868
       22.86 -    45.72: 119
       45.72 -    68.57: 20
       68.57 -    91.43: 12
       91.43 -   114.29: 2
  Dihedral angle restraints: 3021
    sinusoidal: 1182
      harmonic: 1839
  Sorted by residual:
  dihedral pdb=" C   TYR A 495 "
           pdb=" N   TYR A 495 "
           pdb=" CA  TYR A 495 "
           pdb=" CB  TYR A 495 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.66  -13.94     0      2.50e+00 1.60e-01 3.11e+01
  dihedral pdb=" N   TYR L 140 "
           pdb=" C   TYR L 140 "
           pdb=" CA  TYR L 140 "
           pdb=" CB  TYR L 140 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.52  -12.72     0      2.50e+00 1.60e-01 2.59e+01
  dihedral pdb=" CA  TYR H  91 "
           pdb=" C   TYR H  91 "
           pdb=" N   CYS H  92 "
           pdb=" CA  CYS H  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.31   24.69     0      5.00e+00 4.00e-02 2.44e+01
  ... (remaining 3018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 595
       0.120 -    0.239: 147
       0.239 -    0.358: 22
       0.358 -    0.477: 4
       0.477 -    0.596: 1
  Chirality restraints: 769
  Sorted by residual:
  chirality pdb=" C1  FUC B   3 "
            pdb=" O6  NAG B   1 "
            pdb=" C2  FUC B   3 "
            pdb=" O5  FUC B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-02 2.50e+03 5.22e+01
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.54    0.14 2.00e-02 2.50e+03 4.89e+01
  chirality pdb=" CA  TYR L 140 "
            pdb=" N   TYR L 140 "
            pdb=" C   TYR L 140 "
            pdb=" CB  TYR L 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 8.89e+00
  ... (remaining 766 not shown)

  Planarity restraints: 886
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  32 "   -0.100 2.00e-02 2.50e+03   5.75e-02 6.62e+01
        pdb=" CG  TYR L  32 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  32 "    0.055 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  32 "    0.043 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  32 "    0.030 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  32 "    0.046 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  32 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR L  32 "   -0.091 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  90 "   -0.075 2.00e-02 2.50e+03   4.78e-02 4.58e+01
        pdb=" CG  TYR H  90 "    0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  90 "    0.035 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  90 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  90 "    0.029 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  90 "    0.043 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  90 "    0.022 2.00e-02 2.50e+03
        pdb=" OH  TYR H  90 "   -0.088 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  91 "    0.093 2.00e-02 2.50e+03   4.74e-02 4.50e+01
        pdb=" CG  TYR L  91 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  91 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  91 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  91 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  91 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  91 "    0.026 2.00e-02 2.50e+03
        pdb=" OH  TYR L  91 "    0.034 2.00e-02 2.50e+03
  ... (remaining 883 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 118
        2.72 -     3.27: 4640
        3.27 -     3.81: 7348
        3.81 -     4.36: 10325
        4.36 -     4.90: 16877
  Nonbonded interactions: 39308
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU L 105 "
            pdb=" OH  TYR L 140 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" CB  GLU H 148 "
            pdb=" CD  PRO H 149 "
     model   vdw
     2.190 3.840
  nonbonded pdb=" OD1 ASP A 442 "
            pdb=" OG  SER H 100B"
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   ARG L 142 "
            pdb=" N   ALA L 144 "
     model   vdw
     2.421 3.120
  nonbonded pdb=" NZ  LYS H 209 "
            pdb=" OE1 GLU L 123 "
     model   vdw
     2.429 3.120
  ... (remaining 39303 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 individual isotropic
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:             9.010
  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:             0.020
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.320
  Find NCS groups from input model:        0.030
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
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      :  0.013   0.081   5058  Z= 0.736
  Angle     :  1.883  13.479   6895  Z= 1.230
  Chirality :  0.106   0.596    769
  Planarity :  0.012   0.120    885
  Dihedral  : 14.710 114.291   1837
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  1.43 %
    Allowed  :  5.41 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  :  4.77 %
    Favored  : 93.03 %
  Cbeta Deviations :  0.68 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.32), residues: 629
  helix: -3.80 (0.43), residues: 46
  sheet:  0.50 (0.33), residues: 235
  loop : -0.57 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 100A
 TYR   0.100   0.016   TYR L  32 
 PHE   0.063   0.014   PHE H 100G
 TRP   0.063   0.016   TRP L  35 
 HIS   0.010   0.004   HIS L 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.01269 ( 5051)
  covalent geometry    : angle       1.87749 ( 6878)
  SS BOND              : bond        0.00850 (    4)
  SS BOND              : angle       1.23476 (    8)
  hydrogen bonds       : bond        0.14921 (  173)
  hydrogen bonds       : angle       8.87402 (  456)
  link_BETA1-4         : bond        0.02569 (    1)
  link_BETA1-4         : angle       4.15115 (    3)
  link_BETA1-6         : bond        0.03602 (    1)
  link_BETA1-6         : angle       5.37931 (    3)
  link_NAG-ASN         : bond        0.00971 (    1)
  link_NAG-ASN         : angle       4.52525 (    3)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  443 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8640 (p)
REVERT: H  148 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5282 (tt0)
REVERT: L   48 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8753 (mp)
REVERT: L  103 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8838 (mtpp)
REVERT: L  188 LYS cc_start: 0.8859 (ptmm) cc_final: 0.8533 (pttm)
  outliers start: 12
  outliers final: 5
  residues processed: 109
  average time/residue: 0.1046
  time to fit residues: 13.7867
Evaluate side-chains
  82 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  148 GLU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0970
   chunk 61 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.148339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.106553 restraints weight = 6352.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.44
r_work: 0.3085 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5058  Z= 0.167
  Angle     :  0.746  10.282   6895  Z= 0.387
  Chirality :  0.050   0.197    769
  Planarity :  0.005   0.040    885
  Dihedral  : 10.491  93.669    762
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  3.18 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  9.54 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -0.02 (0.34), residues: 629
  helix: -2.97 (0.56), residues: 47
  sheet:  0.84 (0.32), residues: 262
  loop : -0.20 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 108 
 TYR   0.027   0.002   TYR L  91 
 PHE   0.032   0.002   PHE H 146 
 TRP   0.023   0.002   TRP H  50 
 HIS   0.004   0.002   HIS H 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 5051)
  covalent geometry    : angle       0.74446 ( 6878)
  SS BOND              : bond        0.00476 (    4)
  SS BOND              : angle       0.88300 (    8)
  hydrogen bonds       : bond        0.04138 (  173)
  hydrogen bonds       : angle       6.55095 (  456)
  link_BETA1-4         : bond        0.00039 (    1)
  link_BETA1-4         : angle       1.10308 (    3)
  link_BETA1-6         : bond        0.01394 (    1)
  link_BETA1-6         : angle       1.80718 (    3)
  link_NAG-ASN         : bond        0.00367 (    1)
  link_NAG-ASN         : angle       1.11092 (    3)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8049 (mm-30)
REVERT: A  440 ASN cc_start: 0.8496 (p0) cc_final: 0.8023 (t0)
REVERT: A  443 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8838 (p)
REVERT: H  209 LYS cc_start: 0.6755 (tppt) cc_final: 0.6494 (mmtt)
REVERT: L  167 ASP cc_start: 0.8065 (t0) cc_final: 0.7575 (t0)
REVERT: L  183 LYS cc_start: 0.8297 (tptm) cc_final: 0.7771 (tptp)
  outliers start: 9
  outliers final: 5
  residues processed: 101
  average time/residue: 0.0983
  time to fit residues: 12.1825
Evaluate side-chains
  81 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   55 GLU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0270
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7438

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.147090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.108637 restraints weight = 6380.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.30
r_work: 0.3063 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5058  Z= 0.192
  Angle     :  0.711   9.598   6895  Z= 0.357
  Chirality :  0.048   0.182    769
  Planarity :  0.005   0.033    885
  Dihedral  :  8.140  75.061    753
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.93 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 11.56 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.34), residues: 629
  helix: -2.58 (0.59), residues: 52
  sheet:  0.83 (0.33), residues: 259
  loop : -0.26 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 346 
 TYR   0.024   0.002   TYR L  91 
 PHE   0.015   0.002   PHE H 146 
 TRP   0.020   0.002   TRP H  50 
 HIS   0.005   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 5051)
  covalent geometry    : angle       0.70897 ( 6878)
  SS BOND              : bond        0.00399 (    4)
  SS BOND              : angle       0.78468 (    8)
  hydrogen bonds       : bond        0.03477 (  173)
  hydrogen bonds       : angle       5.97337 (  456)
  link_BETA1-4         : bond        0.00321 (    1)
  link_BETA1-4         : angle       1.29845 (    3)
  link_BETA1-6         : bond        0.01981 (    1)
  link_BETA1-6         : angle       2.23617 (    3)
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       1.35945 (    3)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8026 (mm-30)
REVERT: A  440 ASN cc_start: 0.8513 (p0) cc_final: 0.8085 (t0)
REVERT: A  443 SER cc_start: 0.9154 (m) cc_final: 0.8937 (p)
REVERT: A  466 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8260 (ptp90)
REVERT: H   12 LYS cc_start: 0.8269 (mmtt) cc_final: 0.8044 (mmmt)
REVERT: H  148 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6287 (tp30)
REVERT: H  209 LYS cc_start: 0.6896 (tppt) cc_final: 0.6623 (mmtt)
REVERT: L  167 ASP cc_start: 0.8015 (t0) cc_final: 0.7443 (t0)
REVERT: L  183 LYS cc_start: 0.8331 (tptm) cc_final: 0.7688 (tptp)
  outliers start: 15
  outliers final: 9
  residues processed: 87
  average time/residue: 0.0957
  time to fit residues: 10.1799
Evaluate side-chains
  79 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  148 GLU
Chi-restraints excluded: chain H residue  182 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   55 GLU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 9 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
L 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.147735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.106036 restraints weight = 6292.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.42
r_work: 0.3066 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5058  Z= 0.185
  Angle     :  0.674   7.922   6895  Z= 0.336
  Chirality :  0.047   0.167    769
  Planarity :  0.004   0.033    885
  Dihedral  :  7.211  60.819    751
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.66 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.21 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.34), residues: 629
  helix: -2.01 (0.68), residues: 46
  sheet:  0.83 (0.33), residues: 258
  loop : -0.31 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 108 
 TYR   0.022   0.002   TYR L  91 
 PHE   0.017   0.002   PHE H 146 
 TRP   0.017   0.002   TRP H  50 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 5051)
  covalent geometry    : angle       0.67147 ( 6878)
  SS BOND              : bond        0.00376 (    4)
  SS BOND              : angle       0.71137 (    8)
  hydrogen bonds       : bond        0.03173 (  173)
  hydrogen bonds       : angle       5.72689 (  456)
  link_BETA1-4         : bond        0.00369 (    1)
  link_BETA1-4         : angle       1.17322 (    3)
  link_BETA1-6         : bond        0.02100 (    1)
  link_BETA1-6         : angle       2.24122 (    3)
  link_NAG-ASN         : bond        0.00110 (    1)
  link_NAG-ASN         : angle       1.52027 (    3)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  440 ASN cc_start: 0.8493 (p0) cc_final: 0.8025 (t0)
REVERT: A  443 SER cc_start: 0.9155 (m) cc_final: 0.8946 (p)
REVERT: A  466 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.7631 (ptp90)
REVERT: H  148 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6494 (tp30)
REVERT: H  209 LYS cc_start: 0.6866 (tppt) cc_final: 0.6650 (tptp)
REVERT: L  167 ASP cc_start: 0.7859 (t0) cc_final: 0.7223 (m-30)
REVERT: L  183 LYS cc_start: 0.8287 (tptm) cc_final: 0.7610 (tptp)
  outliers start: 11
  outliers final: 9
  residues processed: 82
  average time/residue: 0.1151
  time to fit residues: 11.3480
Evaluate side-chains
  77 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue  148 GLU
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain H residue  182 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   55 GLU
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN
L 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.146129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.107296 restraints weight = 6371.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.37
r_work: 0.3019 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   5058  Z= 0.239
  Angle     :  0.716   8.338   6895  Z= 0.353
  Chirality :  0.048   0.163    769
  Planarity :  0.004   0.032    885
  Dihedral  :  6.913  52.568    751
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.45 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 13.58 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.34), residues: 629
  helix: -1.35 (0.81), residues: 40
  sheet:  0.85 (0.32), residues: 260
  loop : -0.27 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 108 
 TYR   0.022   0.002   TYR L  91 
 PHE   0.015   0.002   PHE L  71 
 TRP   0.016   0.002   TRP H  50 
 HIS   0.004   0.001   HIS H 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 ( 5051)
  covalent geometry    : angle       0.71332 ( 6878)
  SS BOND              : bond        0.00361 (    4)
  SS BOND              : angle       0.70977 (    8)
  hydrogen bonds       : bond        0.03317 (  173)
  hydrogen bonds       : angle       5.70950 (  456)
  link_BETA1-4         : bond        0.00275 (    1)
  link_BETA1-4         : angle       1.22722 (    3)
  link_BETA1-6         : bond        0.02187 (    1)
  link_BETA1-6         : angle       2.09337 (    3)
  link_NAG-ASN         : bond        0.00060 (    1)
  link_NAG-ASN         : angle       1.73108 (    3)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  440 ASN cc_start: 0.8542 (p0) cc_final: 0.8070 (t0)
REVERT: A  443 SER cc_start: 0.9146 (m) cc_final: 0.8910 (p)
REVERT: A  466 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.7922 (ptp90)
REVERT: H  148 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6568 (tp30)
REVERT: H  209 LYS cc_start: 0.7044 (tppt) cc_final: 0.6576 (mmtt)
REVERT: L   29 ILE cc_start: 0.8626 (mm) cc_final: 0.8355 (mm)
REVERT: L  167 ASP cc_start: 0.7929 (t0) cc_final: 0.7306 (m-30)
REVERT: L  183 LYS cc_start: 0.8373 (tptm) cc_final: 0.7703 (tptp)
REVERT: L  199 GLN cc_start: 0.8644 (tt0) cc_final: 0.8151 (mt0)
  outliers start: 17
  outliers final: 12
  residues processed: 85
  average time/residue: 0.0890
  time to fit residues: 9.3139
Evaluate side-chains
  82 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  148 GLU
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain H residue  182 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   55 GLU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  164 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0970
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 17 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** 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 = 0.3725 r_free = 0.3725 target = 0.147752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.106223 restraints weight = 6425.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 2.43
r_work: 0.3080 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5058  Z= 0.147
  Angle     :  0.640   7.206   6895  Z= 0.317
  Chirality :  0.045   0.140    769
  Planarity :  0.004   0.033    885
  Dihedral  :  6.421  49.559    751
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  3.34 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.50 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.35), residues: 629
  helix: -1.25 (0.82), residues: 40
  sheet:  0.93 (0.32), residues: 267
  loop : -0.23 (0.37), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 108 
 TYR   0.019   0.002   TYR L  91 
 PHE   0.012   0.001   PHE H 146 
 TRP   0.015   0.002   TRP H  50 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 5051)
  covalent geometry    : angle       0.63823 ( 6878)
  SS BOND              : bond        0.00349 (    4)
  SS BOND              : angle       0.63404 (    8)
  hydrogen bonds       : bond        0.02896 (  173)
  hydrogen bonds       : angle       5.42604 (  456)
  link_BETA1-4         : bond        0.00423 (    1)
  link_BETA1-4         : angle       1.07733 (    3)
  link_BETA1-6         : bond        0.02278 (    1)
  link_BETA1-6         : angle       2.02529 (    3)
  link_NAG-ASN         : bond        0.00216 (    1)
  link_NAG-ASN         : angle       1.53216 (    3)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  440 ASN cc_start: 0.8503 (p0) cc_final: 0.8023 (t0)
REVERT: A  443 SER cc_start: 0.9103 (m) cc_final: 0.8897 (p)
REVERT: A  466 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.7496 (ptp90)
REVERT: H  148 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6462 (tp30)
REVERT: H  209 LYS cc_start: 0.6892 (tppt) cc_final: 0.6489 (mmtt)
REVERT: L   29 ILE cc_start: 0.8580 (mm) cc_final: 0.8324 (mm)
REVERT: L   55 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7232 (tt0)
REVERT: L  167 ASP cc_start: 0.7935 (t0) cc_final: 0.7316 (m-30)
REVERT: L  183 LYS cc_start: 0.8391 (tptm) cc_final: 0.7705 (tptp)
REVERT: L  199 GLN cc_start: 0.8611 (tt0) cc_final: 0.8146 (mt0)
  outliers start: 14
  outliers final: 10
  residues processed: 79
  average time/residue: 0.0933
  time to fit residues: 9.0233
Evaluate side-chains
  78 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  148 GLU
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain H residue  182 VAL
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   55 GLU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  164 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 44 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 15 optimal weight:    0.0980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.147555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.106148 restraints weight = 6311.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.40
r_work: 0.3083 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5058  Z= 0.160
  Angle     :  0.644   7.065   6895  Z= 0.318
  Chirality :  0.045   0.132    769
  Planarity :  0.004   0.033    885
  Dihedral  :  6.204  50.369    751
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.97 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 14.31 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.35), residues: 629
  helix: -1.11 (0.84), residues: 40
  sheet:  0.99 (0.32), residues: 265
  loop : -0.18 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 108 
 TYR   0.022   0.002   TYR H  99 
 PHE   0.011   0.001   PHE H 166 
 TRP   0.015   0.002   TRP H  50 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 5051)
  covalent geometry    : angle       0.64146 ( 6878)
  SS BOND              : bond        0.00334 (    4)
  SS BOND              : angle       0.63088 (    8)
  hydrogen bonds       : bond        0.02909 (  173)
  hydrogen bonds       : angle       5.33089 (  456)
  link_BETA1-4         : bond        0.00505 (    1)
  link_BETA1-4         : angle       1.11328 (    3)
  link_BETA1-6         : bond        0.02190 (    1)
  link_BETA1-6         : angle       1.83138 (    3)
  link_NAG-ASN         : bond        0.00110 (    1)
  link_NAG-ASN         : angle       1.73998 (    3)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  440 ASN cc_start: 0.8504 (p0) cc_final: 0.8042 (t0)
REVERT: A  443 SER cc_start: 0.9116 (m) cc_final: 0.8901 (p)
REVERT: A  466 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.7667 (ptp90)
REVERT: H  148 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6593 (tp30)
REVERT: H  209 LYS cc_start: 0.6929 (tppt) cc_final: 0.6534 (mmtt)
REVERT: L   29 ILE cc_start: 0.8577 (mm) cc_final: 0.8314 (mm)
REVERT: L   55 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7251 (tt0)
REVERT: L  167 ASP cc_start: 0.7921 (t0) cc_final: 0.7298 (m-30)
REVERT: L  183 LYS cc_start: 0.8373 (tptm) cc_final: 0.7687 (tptp)
REVERT: L  199 GLN cc_start: 0.8595 (tt0) cc_final: 0.8162 (mt0)
  outliers start: 17
  outliers final: 13
  residues processed: 82
  average time/residue: 0.1000
  time to fit residues: 9.8577
Evaluate side-chains
  83 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  148 GLU
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  182 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   55 GLU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  146 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 30 optimal weight:    0.2980
   chunk 8 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.148681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.110431 restraints weight = 6379.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.32
r_work: 0.3096 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5058  Z= 0.140
  Angle     :  0.626   6.980   6895  Z= 0.309
  Chirality :  0.045   0.133    769
  Planarity :  0.004   0.031    885
  Dihedral  :  6.007  51.033    751
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.82 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 14.68 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.35), residues: 629
  helix: -1.08 (0.84), residues: 40
  sheet:  1.03 (0.33), residues: 255
  loop : -0.24 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 108 
 TYR   0.022   0.002   TYR H  99 
 PHE   0.009   0.001   PHE H  59 
 TRP   0.015   0.002   TRP H  50 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5051)
  covalent geometry    : angle       0.62436 ( 6878)
  SS BOND              : bond        0.00326 (    4)
  SS BOND              : angle       0.55117 (    8)
  hydrogen bonds       : bond        0.02810 (  173)
  hydrogen bonds       : angle       5.22457 (  456)
  link_BETA1-4         : bond        0.00467 (    1)
  link_BETA1-4         : angle       1.06062 (    3)
  link_BETA1-6         : bond        0.02260 (    1)
  link_BETA1-6         : angle       1.78970 (    3)
  link_NAG-ASN         : bond        0.00233 (    1)
  link_NAG-ASN         : angle       1.67182 (    3)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  440 ASN cc_start: 0.8501 (p0) cc_final: 0.8045 (t0)
REVERT: A  443 SER cc_start: 0.9101 (m) cc_final: 0.8891 (p)
REVERT: H  117 LYS cc_start: 0.8133 (tttt) cc_final: 0.7648 (tttp)
REVERT: H  148 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6669 (tp30)
REVERT: H  209 LYS cc_start: 0.6930 (tppt) cc_final: 0.6530 (mmtt)
REVERT: L   29 ILE cc_start: 0.8569 (mm) cc_final: 0.8333 (mm)
REVERT: L   55 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7206 (tt0)
REVERT: L  167 ASP cc_start: 0.7931 (t0) cc_final: 0.7277 (m-30)
REVERT: L  183 LYS cc_start: 0.8393 (tptm) cc_final: 0.7687 (tptp)
REVERT: L  199 GLN cc_start: 0.8596 (tt0) cc_final: 0.8227 (mt0)
  outliers start: 17
  outliers final: 13
  residues processed: 89
  average time/residue: 0.0877
  time to fit residues: 9.5843
Evaluate side-chains
  82 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  148 GLU
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  182 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   55 GLU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  124 GLN
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  164 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 18 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9980
   chunk 17 optimal weight:    0.2980
   chunk 60 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 52 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.147797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.106100 restraints weight = 6311.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.40
r_work: 0.3081 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5058  Z= 0.181
  Angle     :  0.660   7.040   6895  Z= 0.325
  Chirality :  0.046   0.135    769
  Planarity :  0.004   0.031    885
  Dihedral  :  6.023  51.666    751
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.61 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 14.86 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.35), residues: 629
  helix: -1.13 (0.83), residues: 40
  sheet:  0.98 (0.33), residues: 255
  loop : -0.28 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 108 
 TYR   0.024   0.002   TYR H  99 
 PHE   0.011   0.001   PHE L  71 
 TRP   0.015   0.002   TRP H  50 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 5051)
  covalent geometry    : angle       0.65769 ( 6878)
  SS BOND              : bond        0.00367 (    4)
  SS BOND              : angle       0.61493 (    8)
  hydrogen bonds       : bond        0.02910 (  173)
  hydrogen bonds       : angle       5.23863 (  456)
  link_BETA1-4         : bond        0.00503 (    1)
  link_BETA1-4         : angle       1.13612 (    3)
  link_BETA1-6         : bond        0.02250 (    1)
  link_BETA1-6         : angle       1.70560 (    3)
  link_NAG-ASN         : bond        0.00181 (    1)
  link_NAG-ASN         : angle       1.80651 (    3)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  440 ASN cc_start: 0.8525 (p0) cc_final: 0.8052 (t0)
REVERT: A  466 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.7667 (ptp90)
REVERT: H  148 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6701 (tp30)
REVERT: H  209 LYS cc_start: 0.7005 (tppt) cc_final: 0.6597 (mmtt)
REVERT: L   29 ILE cc_start: 0.8569 (mm) cc_final: 0.8348 (mm)
REVERT: L   55 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7255 (tt0)
REVERT: L  124 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7452 (tp40)
REVERT: L  167 ASP cc_start: 0.7960 (t0) cc_final: 0.7331 (m-30)
REVERT: L  183 LYS cc_start: 0.8383 (tptm) cc_final: 0.7708 (tptp)
REVERT: L  199 GLN cc_start: 0.8587 (tt0) cc_final: 0.8240 (mt0)
  outliers start: 19
  outliers final: 14
  residues processed: 86
  average time/residue: 0.0972
  time to fit residues: 10.1586
Evaluate side-chains
  89 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  148 GLU
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  182 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   55 GLU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  124 GLN
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  164 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0370
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0970
   chunk 29 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.4456

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.148845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.107208 restraints weight = 6390.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.44
r_work: 0.3085 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5058  Z= 0.141
  Angle     :  0.641   6.994   6895  Z= 0.315
  Chirality :  0.045   0.132    769
  Planarity :  0.004   0.032    885
  Dihedral  :  5.957  52.051    751
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.82 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.78 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.35), residues: 629
  helix: -1.11 (0.83), residues: 40
  sheet:  0.97 (0.33), residues: 255
  loop : -0.25 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 108 
 TYR   0.025   0.002   TYR H  99 
 PHE   0.008   0.001   PHE H 166 
 TRP   0.015   0.002   TRP H  50 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5051)
  covalent geometry    : angle       0.63898 ( 6878)
  SS BOND              : bond        0.00336 (    4)
  SS BOND              : angle       0.48482 (    8)
  hydrogen bonds       : bond        0.02785 (  173)
  hydrogen bonds       : angle       5.15475 (  456)
  link_BETA1-4         : bond        0.00551 (    1)
  link_BETA1-4         : angle       1.09106 (    3)
  link_BETA1-6         : bond        0.02210 (    1)
  link_BETA1-6         : angle       1.66643 (    3)
  link_NAG-ASN         : bond        0.00298 (    1)
  link_NAG-ASN         : angle       1.79809 (    3)

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

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

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1258 Ramachandran restraints generated.
    629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  440 ASN cc_start: 0.8524 (p0) cc_final: 0.8049 (t0)
REVERT: A  466 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.7549 (ptp90)
REVERT: H  117 LYS cc_start: 0.8146 (tttt) cc_final: 0.7659 (tttp)
REVERT: H  209 LYS cc_start: 0.6960 (tppt) cc_final: 0.6558 (mmtt)
REVERT: L   29 ILE cc_start: 0.8549 (mm) cc_final: 0.8331 (mm)
REVERT: L   55 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7258 (tt0)
REVERT: L  167 ASP cc_start: 0.7950 (t0) cc_final: 0.7327 (m-30)
REVERT: L  183 LYS cc_start: 0.8389 (tptm) cc_final: 0.7713 (tptp)
REVERT: L  199 GLN cc_start: 0.8567 (tt0) cc_final: 0.8221 (mt0)
  outliers start: 16
  outliers final: 14
  residues processed: 86
  average time/residue: 0.0934
  time to fit residues: 9.7007
Evaluate side-chains
  89 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  182 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   55 GLU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  124 GLN
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  164 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 37 optimal weight:    0.0050
   chunk 6 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
L 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.147892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.106186 restraints weight = 6407.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.42
r_work: 0.3086 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5058  Z= 0.180
  Angle     :  0.663   7.119   6895  Z= 0.325
  Chirality :  0.046   0.136    769
  Planarity :  0.004   0.031    885
  Dihedral  :  6.040  52.625    751
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.61 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.41 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.34), residues: 629
  helix: -1.16 (0.82), residues: 40
  sheet:  0.95 (0.33), residues: 255
  loop : -0.26 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 108 
 TYR   0.039   0.002   TYR H  99 
 PHE   0.011   0.001   PHE L  71 
 TRP   0.015   0.002   TRP H  50 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 5051)
  covalent geometry    : angle       0.66092 ( 6878)
  SS BOND              : bond        0.00337 (    4)
  SS BOND              : angle       0.57426 (    8)
  hydrogen bonds       : bond        0.02896 (  173)
  hydrogen bonds       : angle       5.19661 (  456)
  link_BETA1-4         : bond        0.00497 (    1)
  link_BETA1-4         : angle       1.14204 (    3)
  link_BETA1-6         : bond        0.02144 (    1)
  link_BETA1-6         : angle       1.61877 (    3)
  link_NAG-ASN         : bond        0.00253 (    1)
  link_NAG-ASN         : angle       1.93648 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1668.30 seconds
wall clock time: 29 minutes 13.53 seconds (1753.53 seconds total)