Starting phenix.real_space_refine
on Wed Sep 17 04:02:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zxn_60545/09_2025/8zxn_60545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zxn_60545/09_2025/8zxn_60545.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zxn_60545/09_2025/8zxn_60545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zxn_60545/09_2025/8zxn_60545.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zxn_60545/09_2025/8zxn_60545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zxn_60545/09_2025/8zxn_60545.map"
  }
  resolution = 3.06
  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=   0.001 sd=   0.149
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      15      5.16       5
     C    2414      2.51       5
     N     587      2.21       5
     O     637      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3653
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 3625
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 25, 'TRANS': 445}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.18, per 1000 atoms: 0.32
  Number of scatterers: 3653
  At special positions: 0
  Unit cell: (88.976, 61.088, 70.384, 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      15     16.00
     O     637      8.00
     N     587      7.00
     C    2414      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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 "
    NAG-ASN
      " NAG B   1 " - " ASN A  90 "
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 149.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  856

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      86.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 66
      removed outlier: 3.636A  pdb=" N   LEU A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLY A  66 " --> pdb=" O   ALA A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 77
      removed outlier: 3.760A  pdb=" N   SER A  76 " --> pdb=" O   GLY A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 98
      removed outlier: 3.696A  pdb=" N   ARG A  95 " --> pdb=" O   GLU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 132
      removed outlier: 4.756A  pdb=" N   PHE A 117 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   ALA A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ILE A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   LYS A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 144
    Processing helix  chain 'A' and resid 144 through 157
      removed outlier: 3.530A  pdb=" N   ALA A 148 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 162
    Processing helix  chain 'A' and resid 164 through 193
      Proline residue:  A 186  - end of helix
      removed outlier: 3.567A  pdb=" N   SER A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 198
      removed outlier: 3.819A  pdb=" N   ARG A 198 " --> pdb=" O   LYS A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 220
      removed outlier: 3.873A  pdb=" N   ALA A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 237
      removed outlier: 4.206A  pdb=" N   PHE A 235 " --> pdb=" O   TRP A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 247
      removed outlier: 3.739A  pdb=" N   ALA A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 3.540A  pdb=" N   PHE A 251 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 262
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 282 through 297
    Processing helix  chain 'A' and resid 303 through 310
    Processing helix  chain 'A' and resid 313 through 330
      removed outlier: 3.695A  pdb=" N   GLN A 328 " --> pdb=" O   MET A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 346
      removed outlier: 3.505A  pdb=" N   ILE A 335 " --> pdb=" O   GLY A 331 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TRP A 336 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ASN A 340 " --> pdb=" O   TRP A 336 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   SER A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 376
      removed outlier: 3.593A  pdb=" N   LEU A 358 " --> pdb=" O   PRO A 354 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   SER A 359 " --> pdb=" O   TYR A 355 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   THR A 360 " --> pdb=" O   VAL A 356 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   GLY A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   GLY A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 5.413A  pdb=" N   LEU A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL A 374 " --> pdb=" O   PHE A 370 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLU A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 404
      removed outlier: 3.603A  pdb=" N   LEU A 383 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 428
      removed outlier: 3.711A  pdb=" N   LEU A 414 " --> pdb=" O   TRP A 410 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER A 415 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE A 416 " --> pdb=" O   PRO A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 441
      removed outlier: 3.825A  pdb=" N   ILE A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 477
      removed outlier: 3.600A  pdb=" N   ILE A 452 " --> pdb=" O   PRO A 448 " (cutoff:3.500A)
      Proline residue:  A 470  - end of helix
    Processing helix  chain 'A' and resid 478 through 480
      No H-bonds generated for 'chain 'A' and resid 478 through 480'
    Processing helix  chain 'A' and resid 481 through 499
    Processing helix  chain 'A' and resid 506 through 519
      removed outlier: 3.846A  pdb=" N   GLN A 512 " --> pdb=" O   ALA A 508 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LYS A 516 " --> pdb=" O   GLN A 512 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   ARG A 517 " --> pdb=" O   ALA A 513 " (cutoff:3.500A)

    254 hydrogen bonds defined for protein.
    756 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: 0.65

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 916
        1.34 -     1.47: 1165
        1.47 -     1.59: 1643
        1.59 -     1.72: 0
        1.72 -     1.85: 22
  Bond restraints: 3746
  Sorted by residual:
  bond pdb=" C   ALA A  80 "
       pdb=" N   PRO A  81 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 8.40e-03 1.42e+04 1.54e+01
  bond pdb=" C   ILE A 348 "
       pdb=" N   PRO A 349 "
    ideal  model  delta    sigma   weight residual
    1.329  1.362 -0.033 1.18e-02 7.18e+03 7.70e+00
  bond pdb=" C   LEU A 499 "
       pdb=" N   PRO A 500 "
    ideal  model  delta    sigma   weight residual
    1.329  1.362 -0.033 1.25e-02 6.40e+03 6.82e+00
  bond pdb=" CA  SER A 193 "
       pdb=" CB  SER A 193 "
    ideal  model  delta    sigma   weight residual
    1.526  1.484  0.042 1.73e-02 3.34e+03 5.95e+00
  bond pdb=" C   TRP A 231 "
       pdb=" N   PRO A 232 "
    ideal  model  delta    sigma   weight residual
    1.335  1.365 -0.030 1.28e-02 6.10e+03 5.48e+00
  ... (remaining 3741 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 3622
        1.20 -     2.41: 1137
        2.41 -     3.61: 287
        3.61 -     4.81: 50
        4.81 -     6.01: 9
  Bond angle restraints: 5105
  Sorted by residual:
  angle pdb=" CA  ASP A 102 "
        pdb=" CB  ASP A 102 "
        pdb=" CG  ASP A 102 "
      ideal   model   delta    sigma   weight residual
     112.60  117.85   -5.25 1.00e+00 1.00e+00 2.76e+01
  angle pdb=" CA  ASP A 177 "
        pdb=" CB  ASP A 177 "
        pdb=" CG  ASP A 177 "
      ideal   model   delta    sigma   weight residual
     112.60  117.06   -4.46 1.00e+00 1.00e+00 1.99e+01
  angle pdb=" N   VAL A 213 "
        pdb=" CA  VAL A 213 "
        pdb=" CB  VAL A 213 "
      ideal   model   delta    sigma   weight residual
     110.54  116.55   -6.01 1.36e+00 5.41e-01 1.95e+01
  angle pdb=" CA  PHE A 337 "
        pdb=" CB  PHE A 337 "
        pdb=" CG  PHE A 337 "
      ideal   model   delta    sigma   weight residual
     113.80  118.15   -4.35 1.00e+00 1.00e+00 1.89e+01
  angle pdb=" CA  PHE A 441 "
        pdb=" CB  PHE A 441 "
        pdb=" CG  PHE A 441 "
      ideal   model   delta    sigma   weight residual
     113.80  117.66   -3.86 1.00e+00 1.00e+00 1.49e+01
  ... (remaining 5100 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 2077
       17.88 -    35.75: 95
       35.75 -    53.63: 21
       53.63 -    71.50: 6
       71.50 -    89.38: 5
  Dihedral angle restraints: 2204
    sinusoidal: 861
      harmonic: 1343
  Sorted by residual:
  dihedral pdb=" CA  GLY A 379 "
           pdb=" C   GLY A 379 "
           pdb=" N   ARG A 380 "
           pdb=" CA  ARG A 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.77  -21.23     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  GLY A 432 "
           pdb=" C   GLY A 432 "
           pdb=" N   ILE A 433 "
           pdb=" CA  ILE A 433 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.16  -18.84     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  GLY A 136 "
           pdb=" C   GLY A 136 "
           pdb=" N   ARG A 137 "
           pdb=" CA  ARG A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.32  -17.68     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 2201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 292
       0.048 -    0.097: 196
       0.097 -    0.145: 76
       0.145 -    0.193: 38
       0.193 -    0.242: 4
  Chirality restraints: 606
  Sorted by residual:
  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   -2.31   -0.09 2.00e-02 2.50e+03 2.19e+01
  chirality pdb=" CA  TRP A 231 "
            pdb=" N   TRP A 231 "
            pdb=" C   TRP A 231 "
            pdb=" CB  TRP A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  PRO A 382 "
            pdb=" N   PRO A 382 "
            pdb=" C   PRO A 382 "
            pdb=" CB  PRO A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 603 not shown)

  Planarity restraints: 630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 137 "   -0.338 9.50e-02 1.11e+02   1.52e-01 1.57e+01
        pdb=" NE  ARG A 137 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 137 "    0.026 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 137 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 137 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 336 "    0.046 2.00e-02 2.50e+03   2.36e-02 1.40e+01
        pdb=" CG  TRP A 336 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 336 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 336 "   -0.028 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 336 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 336 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 336 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 336 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 336 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 336 "    0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 110 "   -0.045 2.00e-02 2.50e+03   2.29e-02 1.31e+01
        pdb=" CG  TRP A 110 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 110 "    0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 110 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 110 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 110 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 110 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 110 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 627 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     2.99: 1723
        2.99 -     3.47: 3724
        3.47 -     3.95: 5977
        3.95 -     4.42: 6829
        4.42 -     4.90: 11273
  Nonbonded interactions: 29526
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 191 "
            pdb=" OG  SER A 255 "
     model   vdw
     2.516 3.040
  nonbonded pdb=" OE1 GLU A 440 "
            pdb=" OG1 THR A 502 "
     model   vdw
     2.591 3.040
  nonbonded pdb=" OD1 ASP A 102 "
            pdb=" OG1 THR A 105 "
     model   vdw
     2.598 3.040
  nonbonded pdb=" O   ILE A 335 "
            pdb=" OG1 THR A 339 "
     model   vdw
     2.608 3.040
  nonbonded pdb=" OE2 GLU A 223 "
            pdb=" OH  TYR A 355 "
     model   vdw
     2.613 3.040
  ... (remaining 29521 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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.100
  Find NCS groups from input model:        0.010
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
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      :  0.009   0.045   3748  Z= 0.562
  Angle     :  1.272  12.166   5111  Z= 0.856
  Chirality :  0.076   0.242    606
  Planarity :  0.010   0.152    629
  Dihedral  : 12.395  89.379   1348
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 0.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  2.32 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.05 (0.32), residues: 469
  helix: -2.20 (0.21), residues: 365
  sheet:  None (None), residues: 0
  loop : -0.34 (0.62), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.003   ARG A 137 
 TYR   0.039   0.008   TYR A  84 
 PHE   0.033   0.007   PHE A 337 
 TRP   0.046   0.010   TRP A 336 
 HIS   0.007   0.003   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00849 ( 3746)
  covalent geometry    : angle       1.25544 ( 5105)
  hydrogen bonds       : bond        0.22368 (  254)
  hydrogen bonds       : angle       8.93944 (  756)
  link_BETA1-4         : bond        0.03979 (    1)
  link_BETA1-4         : angle       7.23965 (    3)
  link_NAG-ASN         : bond        0.00840 (    1)
  link_NAG-ASN         : angle       4.52920 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A   91 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6502 (tt0)
REVERT: A  155 MET cc_start: 0.8451 (mtm) cc_final: 0.8169 (mtm)
REVERT: A  271 LYS cc_start: 0.5800 (tttt) cc_final: 0.5413 (tttm)
REVERT: A  285 GLU cc_start: 0.6637 (mm-30) cc_final: 0.6141 (mm-30)
REVERT: A  324 MET cc_start: 0.8583 (mmt) cc_final: 0.8319 (mmm)
REVERT: A  327 TYR cc_start: 0.8366 (t80) cc_final: 0.7996 (t80)
REVERT: A  328 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8027 (mm-40)
REVERT: A  444 GLN cc_start: 0.7872 (tt0) cc_final: 0.7441 (tp40)
  outliers start: 3
  outliers final: 2
  residues processed: 54
  average time/residue: 0.0944
  time to fit residues: 6.0651
Evaluate side-chains
  38 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  339 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0470
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6678

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.123913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.093033 restraints weight = 3879.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 1.98
r_work: 0.2808 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3748  Z= 0.142
  Angle     :  0.619   6.133   5111  Z= 0.318
  Chirality :  0.043   0.150    606
  Planarity :  0.005   0.036    629
  Dihedral  :  5.199  58.215    549
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  3.87 %
    Favored  : 94.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.38), residues: 469
  helix:  0.35 (0.26), residues: 373
  sheet:  None (None), residues: 0
  loop : -0.36 (0.64), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 137 
 TYR   0.011   0.001   TYR A 312 
 PHE   0.010   0.001   PHE A 117 
 TRP   0.013   0.002   TRP A 231 
 HIS   0.002   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3746)
  covalent geometry    : angle       0.61099 ( 5105)
  hydrogen bonds       : bond        0.05002 (  254)
  hydrogen bonds       : angle       4.62451 (  756)
  link_BETA1-4         : bond        0.00015 (    1)
  link_BETA1-4         : angle       1.72779 (    3)
  link_NAG-ASN         : bond        0.00329 (    1)
  link_NAG-ASN         : angle       3.70969 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A   91 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6811 (tt0)
REVERT: A   94 GLU cc_start: 0.6919 (tt0) cc_final: 0.6206 (tm-30)
REVERT: A  155 MET cc_start: 0.8943 (mtm) cc_final: 0.8698 (mtm)
REVERT: A  271 LYS cc_start: 0.6750 (tttt) cc_final: 0.5872 (tttm)
REVERT: A  285 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6369 (mm-30)
REVERT: A  444 GLN cc_start: 0.7713 (tt0) cc_final: 0.7370 (tp40)
  outliers start: 7
  outliers final: 4
  residues processed: 46
  average time/residue: 0.0858
  time to fit residues: 4.7831
Evaluate side-chains
  44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  363 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0170
   chunk 40 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 328 GLN
A 333 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.126047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.095038 restraints weight = 3835.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.99
r_work: 0.2817 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2676 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3748  Z= 0.119
  Angle     :  0.542   5.151   5111  Z= 0.276
  Chirality :  0.041   0.144    606
  Planarity :  0.005   0.034    629
  Dihedral  :  4.766  59.168    548
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  5.41 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.40), residues: 469
  helix:  1.37 (0.28), residues: 373
  sheet:  None (None), residues: 0
  loop : -0.57 (0.62), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 381 
 TYR   0.013   0.001   TYR A 327 
 PHE   0.010   0.001   PHE A 469 
 TRP   0.012   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 3746)
  covalent geometry    : angle       0.53541 ( 5105)
  hydrogen bonds       : bond        0.04011 (  254)
  hydrogen bonds       : angle       4.14242 (  756)
  link_BETA1-4         : bond        0.00314 (    1)
  link_BETA1-4         : angle       1.33371 (    3)
  link_NAG-ASN         : bond        0.00176 (    1)
  link_NAG-ASN         : angle       3.23566 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   91 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6914 (tt0)
REVERT: A  271 LYS cc_start: 0.6733 (tttt) cc_final: 0.5865 (tttm)
REVERT: A  285 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6315 (mm-30)
REVERT: A  444 GLN cc_start: 0.7477 (tt0) cc_final: 0.7231 (tp-100)
  outliers start: 7
  outliers final: 5
  residues processed: 51
  average time/residue: 0.1081
  time to fit residues: 6.4403
Evaluate side-chains
  44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  363 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 41 optimal weight:    0.1980
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  74 ASN
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.124005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.093436 restraints weight = 3798.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 1.98
r_work: 0.2809 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2669 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3748  Z= 0.128
  Angle     :  0.543   5.225   5111  Z= 0.275
  Chirality :  0.041   0.145    606
  Planarity :  0.005   0.033    629
  Dihedral  :  4.688  59.827    548
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  6.96 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.40), residues: 469
  helix:  1.66 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.48 (0.63), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 381 
 TYR   0.010   0.001   TYR A 312 
 PHE   0.010   0.001   PHE A 469 
 TRP   0.011   0.001   TRP A 231 
 HIS   0.005   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3746)
  covalent geometry    : angle       0.53646 ( 5105)
  hydrogen bonds       : bond        0.03966 (  254)
  hydrogen bonds       : angle       4.03930 (  756)
  link_BETA1-4         : bond        0.00417 (    1)
  link_BETA1-4         : angle       1.26452 (    3)
  link_NAG-ASN         : bond        0.00233 (    1)
  link_NAG-ASN         : angle       3.20936 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A   91 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6838 (tt0)
REVERT: A  195 LYS cc_start: 0.8328 (tttt) cc_final: 0.7659 (pttt)
REVERT: A  271 LYS cc_start: 0.6682 (tttt) cc_final: 0.5800 (tttm)
REVERT: A  285 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6193 (mm-30)
REVERT: A  444 GLN cc_start: 0.7424 (tt0) cc_final: 0.7205 (tp40)
  outliers start: 8
  outliers final: 7
  residues processed: 45
  average time/residue: 0.0878
  time to fit residues: 4.8128
Evaluate side-chains
  43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  515 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 5 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 328 GLN
A 333 ASN
A 458 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.124631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.094218 restraints weight = 3845.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 1.99
r_work: 0.2827 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3748  Z= 0.121
  Angle     :  0.533   5.809   5111  Z= 0.267
  Chirality :  0.041   0.142    606
  Planarity :  0.004   0.032    629
  Dihedral  :  4.594  58.894    548
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  5.93 %
    Favored  : 91.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.41), residues: 469
  helix:  1.84 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.43 (0.63), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 381 
 TYR   0.007   0.001   TYR A  84 
 PHE   0.010   0.001   PHE A 469 
 TRP   0.011   0.001   TRP A 231 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3746)
  covalent geometry    : angle       0.52733 ( 5105)
  hydrogen bonds       : bond        0.03762 (  254)
  hydrogen bonds       : angle       3.95825 (  756)
  link_BETA1-4         : bond        0.00339 (    1)
  link_BETA1-4         : angle       1.12964 (    3)
  link_NAG-ASN         : bond        0.00193 (    1)
  link_NAG-ASN         : angle       3.07359 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  195 LYS cc_start: 0.7813 (tttt) cc_final: 0.7300 (pttt)
REVERT: A  262 GLU cc_start: 0.6988 (mp0) cc_final: 0.6623 (mp0)
REVERT: A  271 LYS cc_start: 0.6667 (tttt) cc_final: 0.5807 (tttm)
REVERT: A  285 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6514 (mm-30)
REVERT: A  444 GLN cc_start: 0.7357 (tt0) cc_final: 0.7129 (tp40)
  outliers start: 10
  outliers final: 7
  residues processed: 47
  average time/residue: 0.0856
  time to fit residues: 4.8420
Evaluate side-chains
  43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  515 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0370
   chunk 25 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.4856

-------------------------------------------------------------------------------
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 = 0.3335 r_free = 0.3335 target = 0.125520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.095263 restraints weight = 3897.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.98
r_work: 0.2819 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3748  Z= 0.109
  Angle     :  0.514   5.861   5111  Z= 0.256
  Chirality :  0.040   0.142    606
  Planarity :  0.004   0.032    629
  Dihedral  :  4.483  58.037    548
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  6.70 %
    Favored  : 91.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.41), residues: 469
  helix:  2.01 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.40 (0.64), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 381 
 TYR   0.010   0.001   TYR A 312 
 PHE   0.009   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.003   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3746)
  covalent geometry    : angle       0.50841 ( 5105)
  hydrogen bonds       : bond        0.03456 (  254)
  hydrogen bonds       : angle       3.85259 (  756)
  link_BETA1-4         : bond        0.00368 (    1)
  link_BETA1-4         : angle       1.08097 (    3)
  link_NAG-ASN         : bond        0.00189 (    1)
  link_NAG-ASN         : angle       3.03102 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   78 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8228 (m)
REVERT: A   94 GLU cc_start: 0.6556 (tt0) cc_final: 0.5905 (pt0)
REVERT: A  174 MET cc_start: 0.8732 (tpt) cc_final: 0.8340 (tpt)
REVERT: A  195 LYS cc_start: 0.7881 (tttt) cc_final: 0.7355 (pttt)
REVERT: A  262 GLU cc_start: 0.6718 (mp0) cc_final: 0.6485 (mp0)
REVERT: A  271 LYS cc_start: 0.6643 (tttt) cc_final: 0.5779 (tttm)
REVERT: A  285 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6377 (mm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 47
  average time/residue: 0.0887
  time to fit residues: 5.0087
Evaluate side-chains
  43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  515 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 44 optimal weight:    0.2980
   chunk 35 optimal weight:    0.0970
   overall best weight:    0.5582

-------------------------------------------------------------------------------
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 = 0.3284 r_free = 0.3284 target = 0.120774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.094080 restraints weight = 4100.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.67
r_work: 0.2828 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3748  Z= 0.113
  Angle     :  0.518   6.365   5111  Z= 0.257
  Chirality :  0.040   0.142    606
  Planarity :  0.004   0.030    629
  Dihedral  :  4.492  58.857    548
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  6.19 %
    Favored  : 91.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.41), residues: 469
  helix:  2.05 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.36 (0.64), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 381 
 TYR   0.006   0.001   TYR A  84 
 PHE   0.010   0.001   PHE A 469 
 TRP   0.011   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 3746)
  covalent geometry    : angle       0.51286 ( 5105)
  hydrogen bonds       : bond        0.03511 (  254)
  hydrogen bonds       : angle       3.83733 (  756)
  link_BETA1-4         : bond        0.00330 (    1)
  link_BETA1-4         : angle       1.05465 (    3)
  link_NAG-ASN         : bond        0.00200 (    1)
  link_NAG-ASN         : angle       2.96991 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A   78 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8236 (m)
REVERT: A  174 MET cc_start: 0.8614 (tpt) cc_final: 0.8169 (tpt)
REVERT: A  195 LYS cc_start: 0.7824 (tttt) cc_final: 0.7444 (ptpt)
REVERT: A  271 LYS cc_start: 0.6731 (tttt) cc_final: 0.5861 (tttm)
REVERT: A  285 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6521 (mm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0822
  time to fit residues: 4.6218
Evaluate side-chains
  45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  515 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 18 optimal weight:    0.0070
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5198

-------------------------------------------------------------------------------
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 = 0.3287 r_free = 0.3287 target = 0.120934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.094492 restraints weight = 4056.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 1.65
r_work: 0.2862 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3748  Z= 0.110
  Angle     :  0.518   6.555   5111  Z= 0.256
  Chirality :  0.040   0.141    606
  Planarity :  0.004   0.030    629
  Dihedral  :  4.450  58.465    548
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  6.44 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.43 (0.41), residues: 469
  helix:  2.11 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.30 (0.65), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 381 
 TYR   0.009   0.001   TYR A 312 
 PHE   0.009   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 3746)
  covalent geometry    : angle       0.51259 ( 5105)
  hydrogen bonds       : bond        0.03433 (  254)
  hydrogen bonds       : angle       3.81542 (  756)
  link_BETA1-4         : bond        0.00368 (    1)
  link_BETA1-4         : angle       1.03695 (    3)
  link_NAG-ASN         : bond        0.00185 (    1)
  link_NAG-ASN         : angle       2.93562 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   78 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8309 (m)
REVERT: A  174 MET cc_start: 0.8638 (tpt) cc_final: 0.8184 (tpt)
REVERT: A  195 LYS cc_start: 0.7821 (tttt) cc_final: 0.7471 (ptpt)
REVERT: A  271 LYS cc_start: 0.6798 (tttt) cc_final: 0.5932 (tttm)
REVERT: A  273 PHE cc_start: 0.7570 (m-80) cc_final: 0.6949 (m-80)
REVERT: A  285 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6333 (mm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 46
  average time/residue: 0.0726
  time to fit residues: 4.1648
Evaluate side-chains
  45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  515 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0980
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0970
   chunk 42 optimal weight:    0.3980
   chunk 2 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.3305 r_free = 0.3305 target = 0.122058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.097054 restraints weight = 4013.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.52
r_work: 0.2875 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3748  Z= 0.106
  Angle     :  0.515   6.653   5111  Z= 0.254
  Chirality :  0.040   0.140    606
  Planarity :  0.004   0.030    629
  Dihedral  :  4.409  58.100    548
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  6.70 %
    Favored  : 90.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.41), residues: 469
  helix:  2.17 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.26 (0.65), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 381 
 TYR   0.005   0.001   TYR A  84 
 PHE   0.009   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 3746)
  covalent geometry    : angle       0.51015 ( 5105)
  hydrogen bonds       : bond        0.03316 (  254)
  hydrogen bonds       : angle       3.77320 (  756)
  link_BETA1-4         : bond        0.00380 (    1)
  link_BETA1-4         : angle       1.02796 (    3)
  link_NAG-ASN         : bond        0.00174 (    1)
  link_NAG-ASN         : angle       2.90512 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   78 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8265 (m)
REVERT: A  174 MET cc_start: 0.8559 (tpt) cc_final: 0.8084 (tpt)
REVERT: A  195 LYS cc_start: 0.7848 (tttt) cc_final: 0.7428 (ptpt)
REVERT: A  271 LYS cc_start: 0.6690 (tttt) cc_final: 0.5814 (tttm)
REVERT: A  273 PHE cc_start: 0.7407 (m-80) cc_final: 0.6767 (m-80)
REVERT: A  285 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6335 (mm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0785
  time to fit residues: 4.5113
Evaluate side-chains
  45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  515 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.3288 r_free = 0.3288 target = 0.121021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.095049 restraints weight = 4066.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.61
r_work: 0.2871 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3748  Z= 0.113
  Angle     :  0.526   6.911   5111  Z= 0.258
  Chirality :  0.040   0.141    606
  Planarity :  0.004   0.029    629
  Dihedral  :  4.422  58.678    548
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  7.47 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.51 (0.41), residues: 469
  helix:  2.16 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.27 (0.65), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 381 
 TYR   0.010   0.001   TYR A 312 
 PHE   0.010   0.001   PHE A 469 
 TRP   0.011   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3746)
  covalent geometry    : angle       0.52051 ( 5105)
  hydrogen bonds       : bond        0.03430 (  254)
  hydrogen bonds       : angle       3.81124 (  756)
  link_BETA1-4         : bond        0.00345 (    1)
  link_BETA1-4         : angle       1.00212 (    3)
  link_NAG-ASN         : bond        0.00197 (    1)
  link_NAG-ASN         : angle       2.90520 (    3)

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

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

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  938 Ramachandran restraints generated.
    469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   78 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8315 (m)
REVERT: A   94 GLU cc_start: 0.6638 (tt0) cc_final: 0.5435 (mt-10)
REVERT: A  174 MET cc_start: 0.8632 (tpt) cc_final: 0.8157 (tpt)
REVERT: A  195 LYS cc_start: 0.7887 (tttt) cc_final: 0.7416 (pttt)
REVERT: A  271 LYS cc_start: 0.6794 (tttt) cc_final: 0.5922 (tttm)
REVERT: A  273 PHE cc_start: 0.7544 (m-80) cc_final: 0.6893 (m-80)
REVERT: A  285 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6441 (mm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0725
  time to fit residues: 4.1202
Evaluate side-chains
  45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  515 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0050
   chunk 14 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0770
   overall best weight:    0.4552

-------------------------------------------------------------------------------
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 = 0.3295 r_free = 0.3295 target = 0.121508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.095753 restraints weight = 3969.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.59
r_work: 0.2857 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3748  Z= 0.107
  Angle     :  0.518   6.799   5111  Z= 0.254
  Chirality :  0.040   0.140    606
  Planarity :  0.004   0.029    629
  Dihedral  :  4.378  58.010    548
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  7.47 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.41), residues: 469
  helix:  2.23 (0.28), residues: 372
  sheet:  None (None), residues: 0
  loop : -0.24 (0.66), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 381 
 TYR   0.005   0.001   TYR A  84 
 PHE   0.009   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 231 
 HIS   0.002   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 3746)
  covalent geometry    : angle       0.51309 ( 5105)
  hydrogen bonds       : bond        0.03294 (  254)
  hydrogen bonds       : angle       3.76923 (  756)
  link_BETA1-4         : bond        0.00396 (    1)
  link_BETA1-4         : angle       1.01615 (    3)
  link_NAG-ASN         : bond        0.00175 (    1)
  link_NAG-ASN         : angle       2.88470 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1107.81 seconds
wall clock time: 19 minutes 43.15 seconds (1183.15 seconds total)