Starting phenix.real_space_refine
on Sun Apr  5 00:53:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dlk_27504/04_2026/8dlk_27504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dlk_27504/04_2026/8dlk_27504.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dlk_27504/04_2026/8dlk_27504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dlk_27504/04_2026/8dlk_27504.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dlk_27504/04_2026/8dlk_27504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dlk_27504/04_2026/8dlk_27504.cif"
  }
  resolution = 3.04
  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=   0.033
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      37      5.16       5
     C    4191      2.51       5
     N    1077      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6554
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1594
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 1.58, per 1000 atoms: 0.24
  Number of scatterers: 6554
  At special positions: 0
  Unit cell: (78, 84, 122, 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      37     16.00
     O    1249      8.00
     N    1077      7.00
     C    4191      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 530 " - pdb=" SG  CYS E 542 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG E 701 " - " ASN E  53 "
      " NAG E 702 " - " ASN E  90 "
      " NAG E 703 " - " ASN E 103 "
      " NAG E 704 " - " ASN E 322 "
      " NAG E 705 " - " ASN E 432 "
      " NAG E 706 " - " ASN E 546 "
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 236.8 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 7 sheets defined
      57.2% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 387
      removed outlier: 3.504A  pdb=" N   LYS B 386 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.653A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.714A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
    Processing helix  chain 'E' and resid 82 through 83
      No H-bonds generated for 'chain 'E' and resid 82 through 83'
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.747A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 101
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 4.089A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 147 through 155
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.681A  pdb=" N   VAL E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 218 through 252
      removed outlier: 3.754A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
    Processing helix  chain 'E' and resid 265 through 267
      No H-bonds generated for 'chain 'E' and resid 265 through 267'
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.819A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 301
    Processing helix  chain 'E' and resid 303 through 318
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.550A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.668A  pdb=" N   TYR E 385 " --> pdb=" O   TYR E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.281A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
      removed outlier: 3.529A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.326A  pdb=" N   PHE E 452 " --> pdb=" O   GLY E 448 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 471
      No H-bonds generated for 'chain 'E' and resid 469 through 471'
    Processing helix  chain 'E' and resid 472 through 484
    Processing helix  chain 'E' and resid 499 through 502
      removed outlier: 3.652A  pdb=" N   SER E 502 " --> pdb=" O   ASP E 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 499 through 502'
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 512 through 533
      removed outlier: 4.465A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.873A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.961A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132
      removed outlier: 3.670A  pdb=" N   LEU E 142 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263
      removed outlier: 6.081A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.381A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    918 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: 0.93

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2081
        1.35 -     1.47: 1806
        1.47 -     1.60: 2792
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6737
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.462 -0.056 2.00e-02 2.50e+03 7.91e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.36e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.454 -0.048 2.00e-02 2.50e+03 5.80e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.36e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.31e+00
  ... (remaining 6732 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 8726
        1.86 -     3.72: 380
        3.72 -     5.58: 35
        5.58 -     7.45: 10
        7.45 -     9.31: 5
  Bond angle restraints: 9156
  Sorted by residual:
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.36  128.21   -5.85 1.42e+00 4.96e-01 1.70e+01
  angle pdb=" CA  CYS E 141 "
        pdb=" CB  CYS E 141 "
        pdb=" SG  CYS E 141 "
      ideal   model   delta    sigma   weight residual
     114.40  122.71   -8.31 2.30e+00 1.89e-01 1.31e+01
  angle pdb=" CA  ASN E 437 "
        pdb=" CB  ASN E 437 "
        pdb=" CG  ASN E 437 "
      ideal   model   delta    sigma   weight residual
     112.60  116.07   -3.47 1.00e+00 1.00e+00 1.20e+01
  angle pdb=" N   TYR B 495 "
        pdb=" CA  TYR B 495 "
        pdb=" C   TYR B 495 "
      ideal   model   delta    sigma   weight residual
     110.32  104.85    5.47 1.59e+00 3.96e-01 1.18e+01
  angle pdb=" CA  ASN B 360 "
        pdb=" CB  ASN B 360 "
        pdb=" CG  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     112.60  115.83   -3.23 1.00e+00 1.00e+00 1.04e+01
  ... (remaining 9151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 3688
       17.01 -    34.03: 303
       34.03 -    51.04: 51
       51.04 -    68.06: 12
       68.06 -    85.07: 12
  Dihedral angle restraints: 4066
    sinusoidal: 1727
      harmonic: 2339
  Sorted by residual:
  dihedral pdb=" CB  CYS E 133 "
           pdb=" SG  CYS E 133 "
           pdb=" SG  CYS E 141 "
           pdb=" CB  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -44.29  -41.71     1      1.00e+01 1.00e-02 2.43e+01
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   16.72   62.28     1      2.00e+01 2.50e-03 1.28e+01
  dihedral pdb=" C   ASN B 360 "
           pdb=" N   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.83    8.23     0      2.50e+00 1.60e-01 1.08e+01
  ... (remaining 4063 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 688
       0.053 -    0.105: 213
       0.105 -    0.158: 63
       0.158 -    0.211: 12
       0.211 -    0.263: 2
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  ASN E 437 "
            pdb=" N   ASN E 437 "
            pdb=" C   ASN E 437 "
            pdb=" CB  ASN E 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.20 2.00e-01 2.50e+01 9.54e-01
  ... (remaining 975 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 145 "   -0.049 5.00e-02 4.00e+02   7.34e-02 8.62e+00
        pdb=" N   PRO E 146 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO E 146 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO E 146 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.047 5.00e-02 4.00e+02   7.06e-02 7.97e+00
        pdb=" N   PRO E 590 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.013 2.00e-02 2.50e+03   2.71e-02 7.32e+00
        pdb=" C   ARG E 169 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ARG E 169 "    0.017 2.00e-02 2.50e+03
        pdb=" N   SER E 170 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 2062
        2.83 -     3.35: 6013
        3.35 -     3.87: 11403
        3.87 -     4.38: 12820
        4.38 -     4.90: 22189
  Nonbonded interactions: 54487
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.351 3.120
  ... (remaining 54482 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:             4.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.420
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
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      :  0.005   0.070   6750  Z= 0.247
  Angle     :  0.891  12.289   9189  Z= 0.488
  Chirality :  0.057   0.263    978
  Planarity :  0.007   0.073   1177
  Dihedral  : 13.416  85.073   2548
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.71 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.26), residues: 793
  helix:  0.45 (0.22), residues: 392
  sheet:  0.65 (0.65), residues: 53
  loop : -0.52 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 460 
 TYR   0.037   0.002   TYR E 385 
 PHE   0.030   0.003   PHE E 369 
 TRP   0.016   0.002   TRP E 566 
 HIS   0.004   0.001   HIS E 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 6737)
  covalent geometry    : angle       0.86060 ( 9156)
  SS BOND              : bond        0.00591 (    6)
  SS BOND              : angle       2.65442 (   12)
  hydrogen bonds       : bond        0.13596 (  322)
  hydrogen bonds       : angle       6.15472 (  918)
  link_NAG-ASN         : bond        0.00826 (    7)
  link_NAG-ASN         : angle       4.49393 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8470 (m-30) cc_final: 0.8183 (m-30)
REVERT: B  519 HIS cc_start: 0.8500 (m170) cc_final: 0.8233 (p90)
REVERT: E  564 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8614 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 97
  average time/residue: 0.1072
  time to fit residues: 13.2066
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   34 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
E 149 ASN
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.060677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.045086 restraints weight = 21287.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 3.58
r_work: 0.2596 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   6750  Z= 0.289
  Angle     :  0.667   7.419   9189  Z= 0.342
  Chirality :  0.045   0.181    978
  Planarity :  0.005   0.041   1177
  Dihedral  :  5.656  51.795   1015
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  7.71 %
    Favored  : 90.86 %
  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:  1.11 (0.28), residues: 793
  helix:  1.36 (0.25), residues: 391
  sheet:  0.60 (0.65), residues: 53
  loop :  0.17 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 357 
 TYR   0.021   0.001   TYR E 385 
 PHE   0.025   0.002   PHE E 400 
 TRP   0.018   0.002   TRP E 165 
 HIS   0.005   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 ( 6737)
  covalent geometry    : angle       0.64692 ( 9156)
  SS BOND              : bond        0.00402 (    6)
  SS BOND              : angle       1.96881 (   12)
  hydrogen bonds       : bond        0.05048 (  322)
  hydrogen bonds       : angle       4.84068 (  918)
  link_NAG-ASN         : bond        0.00389 (    7)
  link_NAG-ASN         : angle       3.15358 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.9179 (t80) cc_final: 0.8955 (t80)
REVERT: B  405 ASP cc_start: 0.8868 (m-30) cc_final: 0.8612 (m-30)
REVERT: B  420 ASP cc_start: 0.9053 (m-30) cc_final: 0.8840 (m-30)
REVERT: B  519 HIS cc_start: 0.8940 (m170) cc_final: 0.8395 (p90)
REVERT: E  114 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9340 (mmmt)
REVERT: E  148 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8327 (mm)
REVERT: E  534 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8953 (mmmt)
  outliers start: 10
  outliers final: 5
  residues processed: 63
  average time/residue: 0.0876
  time to fit residues: 7.5772
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
E 374 HIS
** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.062145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.046732 restraints weight = 20808.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 3.52
r_work: 0.2674 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6750  Z= 0.145
  Angle     :  0.534   6.344   9189  Z= 0.272
  Chirality :  0.041   0.135    978
  Planarity :  0.004   0.035   1177
  Dihedral  :  5.035  52.419   1013
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.86 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.29), residues: 793
  helix:  1.57 (0.25), residues: 398
  sheet:  1.06 (0.74), residues: 43
  loop :  0.28 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 408 
 TYR   0.014   0.001   TYR E 385 
 PHE   0.018   0.001   PHE E 369 
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6737)
  covalent geometry    : angle       0.51567 ( 9156)
  SS BOND              : bond        0.00409 (    6)
  SS BOND              : angle       1.86238 (   12)
  hydrogen bonds       : bond        0.04311 (  322)
  hydrogen bonds       : angle       4.57672 (  918)
  link_NAG-ASN         : bond        0.00407 (    7)
  link_NAG-ASN         : angle       2.63172 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8921 (ptmm)
REVERT: B  405 ASP cc_start: 0.8917 (m-30) cc_final: 0.8662 (m-30)
REVERT: B  519 HIS cc_start: 0.8914 (m170) cc_final: 0.8234 (p90)
REVERT: E  114 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9349 (mmmt)
REVERT: E  332 MET cc_start: 0.8976 (ttp) cc_final: 0.8617 (ttt)
REVERT: E  534 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8951 (mmmt)
  outliers start: 8
  outliers final: 3
  residues processed: 59
  average time/residue: 0.0852
  time to fit residues: 6.8604
Evaluate side-chains
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  386 LYS
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** E 522 GLN ** 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 = 0.3180 r_free = 0.3180 target = 0.060815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.045487 restraints weight = 21285.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 3.53
r_work: 0.2599 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6750  Z= 0.222
  Angle     :  0.571   6.371   9189  Z= 0.292
  Chirality :  0.042   0.147    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  5.014  53.032   1013
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.43 %
    Favored  : 88.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.30), residues: 793
  helix:  1.70 (0.26), residues: 390
  sheet:  0.70 (0.68), residues: 53
  loop :  0.37 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 457 
 TYR   0.018   0.001   TYR E 385 
 PHE   0.020   0.001   PHE E 369 
 TRP   0.016   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 6737)
  covalent geometry    : angle       0.55728 ( 9156)
  SS BOND              : bond        0.00375 (    6)
  SS BOND              : angle       1.64368 (   12)
  hydrogen bonds       : bond        0.04553 (  322)
  hydrogen bonds       : angle       4.57246 (  918)
  link_NAG-ASN         : bond        0.00309 (    7)
  link_NAG-ASN         : angle       2.44213 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B  519 HIS cc_start: 0.8979 (m170) cc_final: 0.8264 (p90)
REVERT: E  114 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9376 (mmmt)
REVERT: E  332 MET cc_start: 0.9007 (ttp) cc_final: 0.8599 (ttp)
REVERT: E  534 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8938 (mmmt)
REVERT: E  613 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6812 (m-80)
  outliers start: 13
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0887
  time to fit residues: 7.4374
Evaluate side-chains
  51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 1 optimal weight:    0.1980
   chunk 46 optimal weight:    0.0060
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0970
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.3994

-------------------------------------------------------------------------------
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 = 0.3231 r_free = 0.3231 target = 0.063071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.047856 restraints weight = 21194.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 3.50
r_work: 0.2700 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6750  Z= 0.109
  Angle     :  0.510   5.715   9189  Z= 0.257
  Chirality :  0.040   0.157    978
  Planarity :  0.004   0.035   1177
  Dihedral  :  4.609  53.800   1013
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.00 %
    Favored  : 86.86 %
  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:  1.58 (0.29), residues: 793
  helix:  1.78 (0.26), residues: 391
  sheet:  1.03 (0.78), residues: 43
  loop :  0.33 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 457 
 TYR   0.010   0.001   TYR E 385 
 PHE   0.014   0.001   PHE E 369 
 TRP   0.012   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6737)
  covalent geometry    : angle       0.49654 ( 9156)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       1.56480 (   12)
  hydrogen bonds       : bond        0.03915 (  322)
  hydrogen bonds       : angle       4.37327 (  918)
  link_NAG-ASN         : bond        0.00368 (    7)
  link_NAG-ASN         : angle       2.18758 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.246 
Fit side-chains
REVERT: B  387 LEU cc_start: 0.9315 (mp) cc_final: 0.9090 (mt)
REVERT: B  405 ASP cc_start: 0.9089 (m-30) cc_final: 0.8863 (m-30)
REVERT: B  417 LYS cc_start: 0.9341 (mmtm) cc_final: 0.9120 (mmtm)
REVERT: B  519 HIS cc_start: 0.8977 (m170) cc_final: 0.8268 (p90)
REVERT: E  114 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9372 (mmmt)
REVERT: E  332 MET cc_start: 0.8965 (ttp) cc_final: 0.8626 (ttp)
REVERT: E  366 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8242 (ttm)
REVERT: E  534 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8965 (mmmt)
REVERT: E  613 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6717 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 56
  average time/residue: 0.0792
  time to fit residues: 6.2678
Evaluate side-chains
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  611 SER
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3205 r_free = 0.3205 target = 0.061851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.046504 restraints weight = 21228.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 3.53
r_work: 0.2664 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6750  Z= 0.155
  Angle     :  0.521   5.839   9189  Z= 0.264
  Chirality :  0.041   0.150    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  4.572  54.341   1013
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.43 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.30), residues: 793
  helix:  1.86 (0.26), residues: 391
  sheet:  0.98 (0.79), residues: 43
  loop :  0.46 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 457 
 TYR   0.015   0.001   TYR B 365 
 PHE   0.016   0.001   PHE E 369 
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6737)
  covalent geometry    : angle       0.50999 ( 9156)
  SS BOND              : bond        0.00335 (    6)
  SS BOND              : angle       1.46566 (   12)
  hydrogen bonds       : bond        0.04131 (  322)
  hydrogen bonds       : angle       4.35254 (  918)
  link_NAG-ASN         : bond        0.00275 (    7)
  link_NAG-ASN         : angle       2.09053 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.248 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8221 (mmtm)
REVERT: B  387 LEU cc_start: 0.9221 (mp) cc_final: 0.8899 (mt)
REVERT: B  405 ASP cc_start: 0.9109 (m-30) cc_final: 0.8822 (m-30)
REVERT: B  417 LYS cc_start: 0.9331 (mmtm) cc_final: 0.9120 (mmtm)
REVERT: B  519 HIS cc_start: 0.8998 (m170) cc_final: 0.8314 (p90)
REVERT: E  114 LYS cc_start: 0.9683 (mmmt) cc_final: 0.9368 (mmmt)
REVERT: E  190 MET cc_start: 0.8959 (tmm) cc_final: 0.8670 (tmm)
REVERT: E  291 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8701 (mp)
REVERT: E  332 MET cc_start: 0.9046 (ttp) cc_final: 0.8574 (ttp)
REVERT: E  383 MET cc_start: 0.9314 (mtm) cc_final: 0.8955 (mtt)
REVERT: E  534 LYS cc_start: 0.9232 (mmmt) cc_final: 0.8970 (mmmt)
REVERT: E  613 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6726 (m-80)
  outliers start: 11
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0799
  time to fit residues: 6.1097
Evaluate side-chains
  53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3200 r_free = 0.3200 target = 0.061046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.046054 restraints weight = 21361.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 3.47
r_work: 0.2661 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
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      :  0.004   0.027   6750  Z= 0.170
  Angle     :  0.530   6.820   9189  Z= 0.270
  Chirality :  0.041   0.156    978
  Planarity :  0.004   0.033   1177
  Dihedral  :  4.571  54.385   1013
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.00 %
    Favored  : 85.29 %
  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:  1.72 (0.30), residues: 793
  helix:  1.88 (0.26), residues: 389
  sheet:  0.54 (0.69), residues: 53
  loop :  0.52 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 457 
 TYR   0.018   0.001   TYR B 365 
 PHE   0.016   0.001   PHE E 369 
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6737)
  covalent geometry    : angle       0.51902 ( 9156)
  SS BOND              : bond        0.00330 (    6)
  SS BOND              : angle       1.44949 (   12)
  hydrogen bonds       : bond        0.04197 (  322)
  hydrogen bonds       : angle       4.37248 (  918)
  link_NAG-ASN         : bond        0.00263 (    7)
  link_NAG-ASN         : angle       2.06949 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.270 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8182 (mmtm)
REVERT: B  387 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8874 (mt)
REVERT: B  405 ASP cc_start: 0.9113 (m-30) cc_final: 0.8838 (m-30)
REVERT: B  417 LYS cc_start: 0.9372 (mmtm) cc_final: 0.9151 (mmtm)
REVERT: B  484 GLU cc_start: 0.8634 (tt0) cc_final: 0.8006 (tp30)
REVERT: B  519 HIS cc_start: 0.8995 (m170) cc_final: 0.8341 (p90)
REVERT: E  190 MET cc_start: 0.8988 (tmm) cc_final: 0.8696 (tmm)
REVERT: E  332 MET cc_start: 0.9103 (ttp) cc_final: 0.8630 (ttp)
REVERT: E  383 MET cc_start: 0.9343 (mtm) cc_final: 0.9031 (mtt)
REVERT: E  470 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8858 (mtpp)
REVERT: E  534 LYS cc_start: 0.9287 (mmmt) cc_final: 0.9028 (mmmt)
REVERT: E  613 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6729 (m-80)
  outliers start: 12
  outliers final: 7
  residues processed: 53
  average time/residue: 0.0791
  time to fit residues: 5.9444
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   82 MET
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  470 LYS
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0170
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    0.3980
   chunk 42 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.8222

-------------------------------------------------------------------------------
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 = 0.3226 r_free = 0.3226 target = 0.061943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.046960 restraints weight = 21384.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 3.51
r_work: 0.2691 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6750  Z= 0.138
  Angle     :  0.511   5.927   9189  Z= 0.258
  Chirality :  0.040   0.156    978
  Planarity :  0.004   0.033   1177
  Dihedral  :  4.492  54.575   1013
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.86 %
    Favored  : 84.43 %
  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:  1.72 (0.30), residues: 793
  helix:  1.81 (0.26), residues: 396
  sheet:  0.78 (0.79), residues: 43
  loop :  0.54 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 457 
 TYR   0.017   0.001   TYR B 365 
 PHE   0.015   0.001   PHE E 369 
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6737)
  covalent geometry    : angle       0.49989 ( 9156)
  SS BOND              : bond        0.00321 (    6)
  SS BOND              : angle       1.40007 (   12)
  hydrogen bonds       : bond        0.04001 (  322)
  hydrogen bonds       : angle       4.31965 (  918)
  link_NAG-ASN         : bond        0.00271 (    7)
  link_NAG-ASN         : angle       2.02723 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.243 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.8533 (mmmm) cc_final: 0.8150 (mmtm)
REVERT: B  405 ASP cc_start: 0.9131 (m-30) cc_final: 0.8850 (m-30)
REVERT: B  417 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9151 (mmtm)
REVERT: B  484 GLU cc_start: 0.8645 (tt0) cc_final: 0.7991 (tp30)
REVERT: B  519 HIS cc_start: 0.9042 (m170) cc_final: 0.8329 (p90)
REVERT: E  190 MET cc_start: 0.8987 (tmm) cc_final: 0.8691 (tmm)
REVERT: E  332 MET cc_start: 0.9081 (ttp) cc_final: 0.8600 (ttp)
REVERT: E  383 MET cc_start: 0.9275 (mtm) cc_final: 0.8981 (mtt)
REVERT: E  534 LYS cc_start: 0.9284 (mmmt) cc_final: 0.9026 (mmmt)
  outliers start: 12
  outliers final: 7
  residues processed: 54
  average time/residue: 0.0795
  time to fit residues: 6.1579
Evaluate side-chains
  53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3179 r_free = 0.3179 target = 0.059927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.044957 restraints weight = 21854.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 3.49
r_work: 0.2652 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   6750  Z= 0.251
  Angle     :  0.608   8.405   9189  Z= 0.310
  Chirality :  0.044   0.148    978
  Planarity :  0.004   0.033   1177
  Dihedral  :  4.761  54.147   1013
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.14 %
    Favored  : 84.43 %
  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:  1.64 (0.30), residues: 793
  helix:  1.72 (0.26), residues: 397
  sheet:  0.32 (0.69), residues: 53
  loop :  0.61 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 245 
 TYR   0.019   0.001   TYR E 385 
 PHE   0.018   0.001   PHE E 369 
 TRP   0.017   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 6737)
  covalent geometry    : angle       0.59814 ( 9156)
  SS BOND              : bond        0.00380 (    6)
  SS BOND              : angle       1.45606 (   12)
  hydrogen bonds       : bond        0.04573 (  322)
  hydrogen bonds       : angle       4.46947 (  918)
  link_NAG-ASN         : bond        0.00224 (    7)
  link_NAG-ASN         : angle       2.15797 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8266 (mmtm)
REVERT: B  405 ASP cc_start: 0.9102 (m-30) cc_final: 0.8759 (m-30)
REVERT: B  519 HIS cc_start: 0.9024 (m170) cc_final: 0.8323 (p90)
REVERT: E  190 MET cc_start: 0.8974 (tmm) cc_final: 0.8673 (tmm)
REVERT: E  470 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8813 (mtpp)
REVERT: E  534 LYS cc_start: 0.9319 (mmmt) cc_final: 0.9023 (mmmt)
REVERT: E  613 TYR cc_start: 0.6959 (t80) cc_final: 0.6403 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 53
  average time/residue: 0.0791
  time to fit residues: 5.9059
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  470 LYS
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  610 TRP
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 74 optimal weight:    0.2980
   chunk 69 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3268 r_free = 0.3268 target = 0.063146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.048256 restraints weight = 21317.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 3.51
r_work: 0.2709 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6750  Z= 0.126
  Angle     :  0.539   7.936   9189  Z= 0.272
  Chirality :  0.040   0.158    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  4.498  54.283   1013
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 14.57 %
    Favored  : 84.43 %
  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:  1.72 (0.30), residues: 793
  helix:  1.78 (0.26), residues: 397
  sheet:  0.64 (0.78), residues: 43
  loop :  0.61 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 457 
 TYR   0.010   0.001   TYR E 385 
 PHE   0.015   0.001   PHE E 369 
 TRP   0.011   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6737)
  covalent geometry    : angle       0.52779 ( 9156)
  SS BOND              : bond        0.00318 (    6)
  SS BOND              : angle       1.39757 (   12)
  hydrogen bonds       : bond        0.03990 (  322)
  hydrogen bonds       : angle       4.34282 (  918)
  link_NAG-ASN         : bond        0.00301 (    7)
  link_NAG-ASN         : angle       2.11098 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8109 (mmtm)
REVERT: B  405 ASP cc_start: 0.9145 (m-30) cc_final: 0.8855 (m-30)
REVERT: B  484 GLU cc_start: 0.8730 (tt0) cc_final: 0.8302 (tp30)
REVERT: B  519 HIS cc_start: 0.9038 (m170) cc_final: 0.8266 (p90)
REVERT: E  190 MET cc_start: 0.8949 (tmm) cc_final: 0.8652 (tmm)
REVERT: E  332 MET cc_start: 0.9068 (ttp) cc_final: 0.8559 (ttp)
REVERT: E  470 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8880 (mtpt)
REVERT: E  534 LYS cc_start: 0.9305 (mmmt) cc_final: 0.8998 (mmmt)
REVERT: E  613 TYR cc_start: 0.6895 (t80) cc_final: 0.6291 (t80)
  outliers start: 7
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0818
  time to fit residues: 6.4032
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  470 LYS
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 63 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3222 r_free = 0.3222 target = 0.062435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.047027 restraints weight = 21034.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 3.52
r_work: 0.2673 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6750  Z= 0.137
  Angle     :  0.536   8.084   9189  Z= 0.271
  Chirality :  0.041   0.156    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  4.460  54.466   1013
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 14.14 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.30), residues: 793
  helix:  1.79 (0.26), residues: 397
  sheet:  0.60 (0.79), residues: 43
  loop :  0.66 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 273 
 TYR   0.011   0.001   TYR E 385 
 PHE   0.015   0.001   PHE E 369 
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6737)
  covalent geometry    : angle       0.52513 ( 9156)
  SS BOND              : bond        0.00329 (    6)
  SS BOND              : angle       1.38511 (   12)
  hydrogen bonds       : bond        0.03998 (  322)
  hydrogen bonds       : angle       4.31882 (  918)
  link_NAG-ASN         : bond        0.00270 (    7)
  link_NAG-ASN         : angle       2.06699 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1564.91 seconds
wall clock time: 27 minutes 33.99 seconds (1653.99 seconds total)