Starting phenix.real_space_refine
on Sat May 10 18:52:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dlk_27504/05_2025/8dlk_27504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dlk_27504/05_2025/8dlk_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_27504/05_2025/8dlk_27504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dlk_27504/05_2025/8dlk_27504.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dlk_27504/05_2025/8dlk_27504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dlk_27504/05_2025/8dlk_27504.cif"
  }
  resolution = 3.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.01, per 1000 atoms: 0.76
  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: 1.35
  Conformation dependent library (CDL) restraints added in 844.6 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: 0.62
  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: 1.80

  Time building geometry restraints manager: 1.64 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:             3.420
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.330
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.740
-------------------------------------------------------------------------------
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 : 2.66
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.016   0.002   TRP E 566 
 HIS   0.004   0.001   HIS E 378 
 PHE   0.030   0.003   PHE E 369 
 TYR   0.037   0.002   TYR E 385 
 ARG   0.012   0.001   ARG E 460 

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

*********************** 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  : 0.683 
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: 0.2309
  time to fit residues: 28.4739
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  : 0.685 
-------------------------------------------------------------------------------
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 66 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3230 r_free = 0.3230 target = 0.063364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.047984 restraints weight = 20686.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 3.54
r_work: 0.2679 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6750  Z= 0.177
  Angle     :  0.591   7.581   9189  Z= 0.299
  Chirality :  0.042   0.151    978
  Planarity :  0.005   0.041   1177
  Dihedral  :  5.352  51.869   1015
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  7.57 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.28), residues: 793
  helix:  1.36 (0.25), residues: 397
  sheet:  1.12 (0.74), residues: 42
  loop : -0.02 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.019   0.001   PHE E 369 
 TYR   0.016   0.001   TYR E 385 
 ARG   0.004   0.001   ARG B 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00422 (    7)
  link_NAG-ASN         : angle       3.09819 (   21)
  hydrogen bonds       : bond        0.04582 (  322)
  hydrogen bonds       : angle       4.70145 (  918)
  SS BOND              : bond        0.00393 (    6)
  SS BOND              : angle       1.99055 (   12)
  covalent geometry    : bond        0.00391 ( 6737)
  covalent geometry    : angle       0.56841 ( 9156)

*********************** 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
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8884 (m-30) cc_final: 0.8494 (m-30)
REVERT: B  484 GLU cc_start: 0.8752 (tt0) cc_final: 0.8465 (tt0)
REVERT: B  519 HIS cc_start: 0.8895 (m170) cc_final: 0.8339 (p90)
REVERT: E  148 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8175 (mt)
  outliers start: 9
  outliers final: 5
  residues processed: 67
  average time/residue: 0.1829
  time to fit residues: 16.7788
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  : 0.687 
-------------------------------------------------------------------------------
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 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.063191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.047731 restraints weight = 20968.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 3.58
r_work: 0.2672 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.2219

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= 0.144
  Angle     :  0.541   6.482   9189  Z= 0.272
  Chirality :  0.041   0.136    978
  Planarity :  0.004   0.037   1177
  Dihedral  :  4.930  53.046   1013
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.29 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.29), residues: 793
  helix:  1.65 (0.26), residues: 391
  sheet:  1.03 (0.75), residues: 43
  loop :  0.19 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.017   0.001   PHE E 369 
 TYR   0.014   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00386 (    7)
  link_NAG-ASN         : angle       2.48572 (   21)
  hydrogen bonds       : bond        0.04225 (  322)
  hydrogen bonds       : angle       4.56747 (  918)
  SS BOND              : bond        0.00384 (    6)
  SS BOND              : angle       1.86344 (   12)
  covalent geometry    : bond        0.00321 ( 6737)
  covalent geometry    : angle       0.52397 ( 9156)

*********************** 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
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8902 (m-30) cc_final: 0.8487 (m-30)
REVERT: B  519 HIS cc_start: 0.8940 (m170) cc_final: 0.8274 (p90)
  outliers start: 9
  outliers final: 2
  residues processed: 58
  average time/residue: 0.1902
  time to fit residues: 15.2665
Evaluate side-chains
  46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  517 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 77 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0870
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.3248 r_free = 0.3248 target = 0.063919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.048589 restraints weight = 21044.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 3.55
r_work: 0.2686 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2415

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= 0.123
  Angle     :  0.507   6.159   9189  Z= 0.256
  Chirality :  0.040   0.131    978
  Planarity :  0.004   0.037   1177
  Dihedral  :  4.658  53.948   1013
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.14 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.29), residues: 793
  helix:  1.82 (0.26), residues: 391
  sheet:  1.12 (0.77), residues: 43
  loop :  0.22 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00347 (    7)
  link_NAG-ASN         : angle       2.17845 (   21)
  hydrogen bonds       : bond        0.03977 (  322)
  hydrogen bonds       : angle       4.41595 (  918)
  SS BOND              : bond        0.00347 (    6)
  SS BOND              : angle       1.67648 (   12)
  covalent geometry    : bond        0.00274 ( 6737)
  covalent geometry    : angle       0.49340 ( 9156)

*********************** 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: 9
    poor density    : 53
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
REVERT: B  519 HIS cc_start: 0.8950 (m170) cc_final: 0.8240 (p90)
REVERT: E  332 MET cc_start: 0.9019 (ttp) cc_final: 0.8685 (ttt)
  outliers start: 9
  outliers final: 6
  residues processed: 60
  average time/residue: 0.1884
  time to fit residues: 15.5129
Evaluate side-chains
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
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  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 20 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0870
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.3243 r_free = 0.3243 target = 0.063619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.048282 restraints weight = 20836.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 3.50
r_work: 0.2709 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.2583

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= 0.130
  Angle     :  0.517   7.239   9189  Z= 0.261
  Chirality :  0.040   0.130    978
  Planarity :  0.003   0.035   1177
  Dihedral  :  4.549  54.627   1013
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.71 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.29), residues: 793
  helix:  1.85 (0.26), residues: 393
  sheet:  1.16 (0.80), residues: 43
  loop :  0.26 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.014   0.001   TYR B 365 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00300 (    7)
  link_NAG-ASN         : angle       2.01725 (   21)
  hydrogen bonds       : bond        0.03981 (  322)
  hydrogen bonds       : angle       4.33113 (  918)
  SS BOND              : bond        0.00309 (    6)
  SS BOND              : angle       1.50951 (   12)
  covalent geometry    : bond        0.00290 ( 6737)
  covalent geometry    : angle       0.50543 ( 9156)

*********************** 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
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
REVERT: B  387 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8983 (mt)
REVERT: B  405 ASP cc_start: 0.9098 (m-30) cc_final: 0.8883 (m-30)
REVERT: B  417 LYS cc_start: 0.9316 (mmtm) cc_final: 0.9095 (mmtm)
REVERT: B  519 HIS cc_start: 0.8952 (m170) cc_final: 0.8249 (p90)
REVERT: E  114 LYS cc_start: 0.9522 (mmmt) cc_final: 0.9277 (pttm)
REVERT: E  332 MET cc_start: 0.9021 (ttp) cc_final: 0.8713 (ttp)
  outliers start: 10
  outliers final: 6
  residues processed: 57
  average time/residue: 0.1804
  time to fit residues: 14.3647
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 31 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3244 r_free = 0.3244 target = 0.063571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.048158 restraints weight = 20866.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 3.57
r_work: 0.2705 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2733

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= 0.126
  Angle     :  0.506   5.774   9189  Z= 0.254
  Chirality :  0.040   0.129    978
  Planarity :  0.003   0.034   1177
  Dihedral  :  4.426  55.125   1013
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.14 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.29), residues: 793
  helix:  1.89 (0.26), residues: 393
  sheet:  1.16 (0.81), residues: 43
  loop :  0.32 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00295 (    7)
  link_NAG-ASN         : angle       1.90447 (   21)
  hydrogen bonds       : bond        0.03905 (  322)
  hydrogen bonds       : angle       4.30099 (  918)
  SS BOND              : bond        0.00320 (    6)
  SS BOND              : angle       1.46037 (   12)
  covalent geometry    : bond        0.00281 ( 6737)
  covalent geometry    : angle       0.49631 ( 9156)

*********************** 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
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: B  387 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8989 (mt)
REVERT: B  405 ASP cc_start: 0.9101 (m-30) cc_final: 0.8819 (m-30)
REVERT: B  417 LYS cc_start: 0.9295 (mmtm) cc_final: 0.9074 (mmtm)
REVERT: B  519 HIS cc_start: 0.8998 (m170) cc_final: 0.8278 (p90)
REVERT: E  332 MET cc_start: 0.8996 (ttp) cc_final: 0.8677 (ttp)
REVERT: E  383 MET cc_start: 0.9329 (mtm) cc_final: 0.9122 (mtt)
  outliers start: 11
  outliers final: 7
  residues processed: 57
  average time/residue: 0.1777
  time to fit residues: 14.1615
Evaluate side-chains
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  503 VAL
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  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 62 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 78 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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**
E 586 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.062341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.046902 restraints weight = 20906.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 3.54
r_work: 0.2654 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6750  Z= 0.150
  Angle     :  0.522   7.940   9189  Z= 0.263
  Chirality :  0.040   0.133    978
  Planarity :  0.003   0.035   1177
  Dihedral  :  4.436  55.189   1013
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.29 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.29), residues: 793
  helix:  1.94 (0.26), residues: 392
  sheet:  1.12 (0.81), residues: 43
  loop :  0.45 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.016   0.001   TYR B 365 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00242 (    7)
  link_NAG-ASN         : angle       1.87840 (   21)
  hydrogen bonds       : bond        0.04033 (  322)
  hydrogen bonds       : angle       4.31890 (  918)
  SS BOND              : bond        0.00318 (    6)
  SS BOND              : angle       1.42581 (   12)
  covalent geometry    : bond        0.00337 ( 6737)
  covalent geometry    : angle       0.51249 ( 9156)

*********************** 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
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8477 (mmmm) cc_final: 0.8078 (mmtm)
REVERT: B  387 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8953 (mt)
REVERT: B  405 ASP cc_start: 0.9135 (m-30) cc_final: 0.8840 (m-30)
REVERT: B  417 LYS cc_start: 0.9254 (mmtm) cc_final: 0.9019 (mmtm)
REVERT: B  472 ILE cc_start: 0.9282 (mm) cc_final: 0.8765 (tp)
REVERT: B  484 GLU cc_start: 0.8683 (tt0) cc_final: 0.7952 (tp30)
REVERT: B  519 HIS cc_start: 0.9045 (m170) cc_final: 0.8261 (p90)
REVERT: E  114 LYS cc_start: 0.9497 (mmmt) cc_final: 0.9204 (mttp)
REVERT: E  190 MET cc_start: 0.8898 (tmm) cc_final: 0.8595 (tmm)
  outliers start: 9
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1871
  time to fit residues: 14.6459
Evaluate side-chains
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  503 VAL
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  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0470
   chunk 33 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.9682

-------------------------------------------------------------------------------
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 = 0.3217 r_free = 0.3217 target = 0.062420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.047070 restraints weight = 21019.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 3.53
r_work: 0.2641 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6750  Z= 0.155
  Angle     :  0.530   6.794   9189  Z= 0.267
  Chirality :  0.041   0.132    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  4.466  55.266   1013
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.14 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.30), residues: 793
  helix:  1.93 (0.26), residues: 391
  sheet:  1.07 (0.81), residues: 43
  loop :  0.52 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00215 (    7)
  link_NAG-ASN         : angle       1.89103 (   21)
  hydrogen bonds       : bond        0.04069 (  322)
  hydrogen bonds       : angle       4.35197 (  918)
  SS BOND              : bond        0.00325 (    6)
  SS BOND              : angle       1.40405 (   12)
  covalent geometry    : bond        0.00350 ( 6737)
  covalent geometry    : angle       0.52026 ( 9156)

*********************** 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
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.750 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8094 (mmtm)
REVERT: B  387 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8975 (mt)
REVERT: B  405 ASP cc_start: 0.9142 (m-30) cc_final: 0.8836 (m-30)
REVERT: B  417 LYS cc_start: 0.9262 (mmtm) cc_final: 0.9048 (mmtm)
REVERT: B  484 GLU cc_start: 0.8705 (tt0) cc_final: 0.8046 (tp30)
REVERT: B  519 HIS cc_start: 0.9034 (m170) cc_final: 0.8288 (p90)
REVERT: E  114 LYS cc_start: 0.9577 (mmmt) cc_final: 0.9287 (mttp)
REVERT: E  190 MET cc_start: 0.8869 (tmm) cc_final: 0.8558 (tmm)
  outliers start: 12
  outliers final: 7
  residues processed: 57
  average time/residue: 0.1841
  time to fit residues: 14.7656
Evaluate side-chains
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  503 VAL
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 8 optimal weight:    0.0030
   chunk 41 optimal weight:    0.0030
   chunk 19 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0570
   chunk 42 optimal weight:    0.8980
   chunk 43 optimal weight:   40.0000
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.3920

-------------------------------------------------------------------------------
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 = 0.3246 r_free = 0.3246 target = 0.063966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.048519 restraints weight = 20820.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 3.55
r_work: 0.2698 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6750  Z= 0.107
  Angle     :  0.508   7.974   9189  Z= 0.253
  Chirality :  0.039   0.131    978
  Planarity :  0.003   0.035   1177
  Dihedral  :  4.300  55.488   1013
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.30), residues: 793
  helix:  1.91 (0.26), residues: 392
  sheet:  1.10 (0.82), residues: 42
  loop :  0.51 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.009   0.001   TYR B 365 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00286 (    7)
  link_NAG-ASN         : angle       1.85980 (   21)
  hydrogen bonds       : bond        0.03708 (  322)
  hydrogen bonds       : angle       4.28368 (  918)
  SS BOND              : bond        0.00359 (    6)
  SS BOND              : angle       1.40230 (   12)
  covalent geometry    : bond        0.00236 ( 6737)
  covalent geometry    : angle       0.49817 ( 9156)

*********************** 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
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.771 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.8432 (mmmm) cc_final: 0.8053 (mmtm)
REVERT: B  405 ASP cc_start: 0.9167 (m-30) cc_final: 0.8878 (m-30)
REVERT: B  472 ILE cc_start: 0.9261 (mm) cc_final: 0.8771 (tp)
REVERT: B  519 HIS cc_start: 0.9016 (m170) cc_final: 0.8239 (p90)
REVERT: E  114 LYS cc_start: 0.9603 (mmmt) cc_final: 0.9319 (mttp)
REVERT: E  332 MET cc_start: 0.9031 (ttp) cc_final: 0.8553 (ttp)
  outliers start: 8
  outliers final: 5
  residues processed: 56
  average time/residue: 0.1796
  time to fit residues: 14.2806
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  : 0.816 
-------------------------------------------------------------------------------
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  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 20 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 19 optimal weight:    0.1980
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3226 r_free = 0.3226 target = 0.062806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.047430 restraints weight = 21138.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 3.55
r_work: 0.2651 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6750  Z= 0.157
  Angle     :  0.554   8.576   9189  Z= 0.275
  Chirality :  0.041   0.172    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  4.388  55.388   1013
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 13.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.30), residues: 793
  helix:  1.90 (0.26), residues: 391
  sheet:  1.11 (0.83), residues: 42
  loop :  0.58 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    7)
  link_NAG-ASN         : angle       1.88425 (   21)
  hydrogen bonds       : bond        0.04058 (  322)
  hydrogen bonds       : angle       4.32730 (  918)
  SS BOND              : bond        0.00342 (    6)
  SS BOND              : angle       1.31770 (   12)
  covalent geometry    : bond        0.00353 ( 6737)
  covalent geometry    : angle       0.54508 ( 9156)

********************** 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
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.693 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8051 (mmtm)
REVERT: B  405 ASP cc_start: 0.9146 (m-30) cc_final: 0.8831 (m-30)
REVERT: B  472 ILE cc_start: 0.9250 (mm) cc_final: 0.8703 (tp)
REVERT: B  484 GLU cc_start: 0.8686 (tt0) cc_final: 0.8268 (tp30)
REVERT: B  519 HIS cc_start: 0.9030 (m170) cc_final: 0.8257 (p90)
REVERT: E  114 LYS cc_start: 0.9611 (mmmt) cc_final: 0.9298 (mttp)
REVERT: E  190 MET cc_start: 0.8873 (tmm) cc_final: 0.8559 (tmm)
  outliers start: 5
  outliers final: 5
  residues processed: 53
  average time/residue: 0.1791
  time to fit residues: 13.3723
Evaluate side-chains
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
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  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 72 optimal weight:    0.3980
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 52 optimal weight:    0.2980
   chunk 30 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3247 r_free = 0.3247 target = 0.063708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.048299 restraints weight = 21140.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 3.56
r_work: 0.2673 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.3061

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= 0.124
  Angle     :  0.534   8.471   9189  Z= 0.264
  Chirality :  0.040   0.167    978
  Planarity :  0.003   0.034   1177
  Dihedral  :  4.334  55.429   1013
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 13.71 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.30), residues: 793
  helix:  1.87 (0.26), residues: 391
  sheet:  1.05 (0.82), residues: 42
  loop :  0.55 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.010   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00266 (    7)
  link_NAG-ASN         : angle       1.86946 (   21)
  hydrogen bonds       : bond        0.03863 (  322)
  hydrogen bonds       : angle       4.30654 (  918)
  SS BOND              : bond        0.00305 (    6)
  SS BOND              : angle       1.26984 (   12)
  covalent geometry    : bond        0.00280 ( 6737)
  covalent geometry    : angle       0.52545 ( 9156)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3117.48 seconds
wall clock time: 54 minutes 51.55 seconds (3291.55 seconds total)