Starting phenix.real_space_refine
on Sat May 10 00:36:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wtu_37842/05_2025/8wtu_37842.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wtu_37842/05_2025/8wtu_37842.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wtu_37842/05_2025/8wtu_37842.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wtu_37842/05_2025/8wtu_37842.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wtu_37842/05_2025/8wtu_37842.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wtu_37842/05_2025/8wtu_37842.cif"
  }
  resolution = 2.7
  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=   0.069
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2918      2.51       5
     N     673      2.21       5
     O     737      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4348
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4334
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 542, 4334
          Classifications: {'peptide': 542}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 522}
          Chain breaks: 1
    Chain: "A"
      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
  Time building chain proxies: 3.56, per 1000 atoms: 0.82
  Number of scatterers: 4348
  At special positions: 0
  Unit cell: (75.65, 67.15, 91.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     737      8.00
     N     673      7.00
     C    2918      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 176 " - pdb=" SG  CYS A 185 " distance=2.03

  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 A 701 " - " ASN A 184 "
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 528.7 milliseconds
  

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  998

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 1 sheets defined
      76.0% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 3.827A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   PHE A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      Proline residue:  A  83  - end of helix
    Processing helix  chain 'A' and resid 94 through 121
      Proline residue:  A 108  - end of helix
      removed outlier: 3.582A  pdb=" N   GLY A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN A 118 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR A 119 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ASN A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 165
      removed outlier: 3.889A  pdb=" N   GLY A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE A 155 " --> pdb=" O   TYR A 151 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A 156 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 191
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 220 through 224
      removed outlier: 3.512A  pdb=" N   GLU A 223 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 251
      removed outlier: 3.544A  pdb=" N   CYS A 240 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL A 243 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 283
      removed outlier: 3.607A  pdb=" N   PHE A 272 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A 279 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 295
      removed outlier: 3.896A  pdb=" N   ALA A 293 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 319
      removed outlier: 4.161A  pdb=" N   TRP A 308 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 338 through 373
      removed outlier: 3.805A  pdb=" N   ASP A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 380
      removed outlier: 4.633A  pdb=" N   ALA A 380 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
      Proline residue:  A 392  - end of helix
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.624A  pdb=" N   TRP A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASP A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   PHE A 435 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 440
    Processing helix  chain 'A' and resid 441 through 458
      removed outlier: 3.659A  pdb=" N   PHE A 445 " --> pdb=" O   HIS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 462
      removed outlier: 3.916A  pdb=" N   THR A 462 " --> pdb=" O   PHE A 459 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 459 through 462'
    Processing helix  chain 'A' and resid 464 through 476
      removed outlier: 4.045A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 496
      removed outlier: 3.634A  pdb=" N   LEU A 482 " --> pdb=" O   GLY A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 510
      removed outlier: 3.599A  pdb=" N   ILE A 505 " --> pdb=" O   PHE A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 523
      removed outlier: 3.527A  pdb=" N   LYS A 522 " --> pdb=" O   ARG A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.630A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   MET A 566 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 580
      removed outlier: 3.572A  pdb=" N   ILE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL A 573 " --> pdb=" O   VAL A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 591
      removed outlier: 3.623A  pdb=" N   GLY A 591 " --> pdb=" O   ARG A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 601
      removed outlier: 3.810A  pdb=" N   HIS A 598 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   HIS A 599 " --> pdb=" O   ASN A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 609
      removed outlier: 3.575A  pdb=" N   PHE A 609 " --> pdb=" O   ILE A 606 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 606 through 609'
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 3.923A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545

    250 hydrogen bonds defined for protein.
    723 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: 1.18

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1264
        1.34 -     1.46: 1123
        1.46 -     1.58: 2071
        1.58 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 4489
  Sorted by residual:
  bond pdb=" C   PHE A  82 "
       pdb=" N   PRO A  83 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 1.51e-02 4.39e+03 2.93e+00
  bond pdb=" CB  PRO A 285 "
       pdb=" CG  PRO A 285 "
    ideal  model  delta    sigma   weight residual
    1.492  1.558 -0.066 5.00e-02 4.00e+02 1.72e+00
  bond pdb=" C5  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.09e+00
  bond pdb=" C3  NAG A 701 "
       pdb=" O3  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.403  1.424 -0.021 2.00e-02 2.50e+03 1.07e+00
  bond pdb=" CA  MET A 107 "
       pdb=" C   MET A 107 "
    ideal  model  delta    sigma   weight residual
    1.521  1.532 -0.011 1.14e-02 7.69e+03 8.98e-01
  ... (remaining 4484 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 6011
        2.00 -     3.99: 99
        3.99 -     5.99: 15
        5.99 -     7.99: 0
        7.99 -     9.98: 1
  Bond angle restraints: 6126
  Sorted by residual:
  angle pdb=" N   VAL A 262 "
        pdb=" CA  VAL A 262 "
        pdb=" C   VAL A 262 "
      ideal   model   delta    sigma   weight residual
     106.21  111.73   -5.52 1.07e+00 8.73e-01 2.66e+01
  angle pdb=" N   VAL A  69 "
        pdb=" CA  VAL A  69 "
        pdb=" C   VAL A  69 "
      ideal   model   delta    sigma   weight residual
     113.47  108.74    4.73 1.01e+00 9.80e-01 2.20e+01
  angle pdb=" N   ILE A 537 "
        pdb=" CA  ILE A 537 "
        pdb=" C   ILE A 537 "
      ideal   model   delta    sigma   weight residual
     111.81  108.41    3.40 8.60e-01 1.35e+00 1.56e+01
  angle pdb=" C   GLY A 106 "
        pdb=" N   MET A 107 "
        pdb=" CA  MET A 107 "
      ideal   model   delta    sigma   weight residual
     119.78  115.17    4.61 1.24e+00 6.50e-01 1.38e+01
  angle pdb=" N   ILE A 592 "
        pdb=" CA  ILE A 592 "
        pdb=" C   ILE A 592 "
      ideal   model   delta    sigma   weight residual
     113.10  109.51    3.59 9.70e-01 1.06e+00 1.37e+01
  ... (remaining 6121 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.46: 2365
       21.46 -    42.92: 127
       42.92 -    64.38: 11
       64.38 -    85.84: 11
       85.84 -   107.30: 8
  Dihedral angle restraints: 2522
    sinusoidal: 954
      harmonic: 1568
  Sorted by residual:
  dihedral pdb=" CB  CYS A 176 "
           pdb=" SG  CYS A 176 "
           pdb=" SG  CYS A 185 "
           pdb=" CB  CYS A 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.08  -41.08     1      1.00e+01 1.00e-02 2.36e+01
  dihedral pdb=" CA  LEU A 252 "
           pdb=" C   LEU A 252 "
           pdb=" N   TRP A 253 "
           pdb=" CA  TRP A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.39  -18.61     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" C2  NAG A 701 "
           pdb=" C3  NAG A 701 "
           pdb=" C4  NAG A 701 "
           pdb=" C5  NAG A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.78  -53.52  107.30     1      3.00e+01 1.11e-03 1.38e+01
  ... (remaining 2519 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 414
       0.032 -    0.065: 206
       0.065 -    0.097: 47
       0.097 -    0.129: 18
       0.129 -    0.162: 3
  Chirality restraints: 688
  Sorted by residual:
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 184 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.53e-01
  chirality pdb=" CA  TYR A 152 "
            pdb=" N   TYR A 152 "
            pdb=" C   TYR A 152 "
            pdb=" CB  TYR A 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  PRO A 513 "
            pdb=" N   PRO A 513 "
            pdb=" C   PRO A 513 "
            pdb=" CB  PRO A 513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 685 not shown)

  Planarity restraints: 744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 103 "   -0.014 2.00e-02 2.50e+03   2.91e-02 8.46e+00
        pdb=" C   ILE A 103 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ILE A 103 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ILE A 104 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 253 "   -0.013 2.00e-02 2.50e+03   1.31e-02 4.30e+00
        pdb=" CG  TRP A 253 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 253 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 253 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 253 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 253 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 253 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 253 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 253 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 253 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 512 "   -0.034 5.00e-02 4.00e+02   5.17e-02 4.28e+00
        pdb=" N   PRO A 513 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 513 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 513 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 741 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1259
        2.82 -     3.34: 3972
        3.34 -     3.86: 6955
        3.86 -     4.38: 8045
        4.38 -     4.90: 14339
  Nonbonded interactions: 34570
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 182 "
            pdb=" OE2 GLU A 212 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" NE2 HIS A 280 "
            pdb=" OG1 THR A 397 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NZ  LYS A 522 "
            pdb=" O   ALA A 616 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" O   ILE A 561 "
            pdb=" OG  SER A 564 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" O   PHE A  72 "
            pdb=" OH  TYR A 271 "
     model   vdw
     2.443 3.040
  ... (remaining 34565 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             2.190
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     15.070
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:11.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
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      :  0.003   0.066   4491  Z= 0.145
  Angle     :  0.679   9.984   6131  Z= 0.441
  Chirality :  0.041   0.162    688
  Planarity :  0.005   0.052    743
  Dihedral  : 15.115 107.297   1521
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  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:  0.10 (0.38), residues: 538
  helix:  0.95 (0.29), residues: 354
  sheet:  None (None), residues: 0
  loop : -1.67 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 222 
 PHE   0.014   0.001   PHE A 335 
 TYR   0.030   0.001   TYR A 152 
 ARG   0.002   0.000   ARG A 587 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00122 (    1)
  link_NAG-ASN         : angle       0.69331 (    3)
  hydrogen bonds       : bond        0.14948 (  250)
  hydrogen bonds       : angle       5.46410 (  723)
  SS BOND              : bond        0.00358 (    1)
  SS BOND              : angle       1.26614 (    2)
  covalent geometry    : bond        0.00270 ( 4489)
  covalent geometry    : angle       0.67837 ( 6126)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7204 (t70) cc_final: 0.6959 (t70)
REVERT: A  206 LYS cc_start: 0.7607 (ptpt) cc_final: 0.7118 (ptmt)
REVERT: A  329 PHE cc_start: 0.7352 (m-80) cc_final: 0.6679 (t80)
REVERT: A  375 ASN cc_start: 0.7708 (m-40) cc_final: 0.7238 (m110)
REVERT: A  528 PHE cc_start: 0.6736 (m-10) cc_final: 0.6427 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 1.1393
  time to fit residues: 106.5206
Evaluate side-chains
  51 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
A 289 ASN
A 292 ASN
A 350 ASN
A 507 GLN
A 555 ASN
A 596 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.136882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.124543 restraints weight = 4434.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 0.78
r_work: 0.3117 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4491  Z= 0.139
  Angle     :  0.576   6.755   6131  Z= 0.297
  Chirality :  0.042   0.174    688
  Planarity :  0.005   0.050    743
  Dihedral  :  6.211  45.102    605
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 1.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.19 %
    Favored  : 89.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.55 (0.38), residues: 538
  helix:  1.27 (0.29), residues: 353
  sheet:  None (None), residues: 0
  loop : -1.43 (0.48), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 253 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.016   0.002   PHE A  94 
 TYR   0.025   0.002   TYR A 111 
 ARG   0.003   0.000   ARG A 301 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00215 (    1)
  link_NAG-ASN         : angle       0.61358 (    3)
  hydrogen bonds       : bond        0.06729 (  250)
  hydrogen bonds       : angle       4.49217 (  723)
  SS BOND              : bond        0.00782 (    1)
  SS BOND              : angle       2.77099 (    2)
  covalent geometry    : bond        0.00273 ( 4489)
  covalent geometry    : angle       0.57417 ( 6126)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.7945 (ptpt) cc_final: 0.7440 (ptmt)
REVERT: A  329 PHE cc_start: 0.8010 (m-80) cc_final: 0.7459 (t80)
REVERT: A  375 ASN cc_start: 0.8046 (m-40) cc_final: 0.7680 (m110)
REVERT: A  381 THR cc_start: 0.8024 (p) cc_final: 0.7738 (t)
REVERT: A  436 GLN cc_start: 0.7887 (mm110) cc_final: 0.7596 (mp-120)
REVERT: A  586 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7758 (mt-10)
  outliers start: 7
  outliers final: 2
  residues processed: 55
  average time/residue: 1.0563
  time to fit residues: 60.7594
Evaluate side-chains
  52 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  586 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN
A 350 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.136127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.123984 restraints weight = 4487.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 0.76
r_work: 0.3103 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4491  Z= 0.133
  Angle     :  0.537   6.312   6131  Z= 0.283
  Chirality :  0.040   0.131    688
  Planarity :  0.005   0.049    743
  Dihedral  :  4.514  26.935    605
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  9.19 %
    Favored  : 88.62 %
  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:  0.75 (0.38), residues: 538
  helix:  1.51 (0.29), residues: 346
  sheet:  None (None), residues: 0
  loop : -1.44 (0.46), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 553 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.014   0.001   PHE A 409 
 TYR   0.017   0.002   TYR A 111 
 ARG   0.002   0.000   ARG A 301 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00429 (    1)
  link_NAG-ASN         : angle       1.41765 (    3)
  hydrogen bonds       : bond        0.06612 (  250)
  hydrogen bonds       : angle       4.44348 (  723)
  SS BOND              : bond        0.00554 (    1)
  SS BOND              : angle       2.58118 (    2)
  covalent geometry    : bond        0.00260 ( 4489)
  covalent geometry    : angle       0.53439 ( 6126)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.7919 (ptpt) cc_final: 0.7324 (pttt)
REVERT: A  329 PHE cc_start: 0.7996 (m-80) cc_final: 0.7486 (t80)
REVERT: A  375 ASN cc_start: 0.8079 (m-40) cc_final: 0.7720 (m110)
REVERT: A  381 THR cc_start: 0.8026 (p) cc_final: 0.7774 (t)
REVERT: A  436 GLN cc_start: 0.7889 (mm110) cc_final: 0.7612 (mp-120)
REVERT: A  586 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7676 (mt-10)
  outliers start: 10
  outliers final: 3
  residues processed: 54
  average time/residue: 1.1818
  time to fit residues: 66.4643
Evaluate side-chains
  51 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  586 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 14 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 350 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.135640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.123061 restraints weight = 4503.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 0.80
r_work: 0.3101 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4491  Z= 0.127
  Angle     :  0.515   6.071   6131  Z= 0.273
  Chirality :  0.040   0.123    688
  Planarity :  0.005   0.051    743
  Dihedral  :  4.190  21.566    605
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 10.28 %
    Favored  : 86.87 %
  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:  0.97 (0.38), residues: 538
  helix:  1.69 (0.29), residues: 345
  sheet:  None (None), residues: 0
  loop : -1.33 (0.46), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 553 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.014   0.001   PHE A 409 
 TYR   0.016   0.002   TYR A  84 
 ARG   0.002   0.000   ARG A 301 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00296 (    1)
  link_NAG-ASN         : angle       1.10843 (    3)
  hydrogen bonds       : bond        0.06370 (  250)
  hydrogen bonds       : angle       4.38124 (  723)
  SS BOND              : bond        0.00532 (    1)
  SS BOND              : angle       2.49859 (    2)
  covalent geometry    : bond        0.00247 ( 4489)
  covalent geometry    : angle       0.51299 ( 6126)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.7912 (ptpt) cc_final: 0.7314 (pttt)
REVERT: A  329 PHE cc_start: 0.8023 (m-80) cc_final: 0.7521 (t80)
REVERT: A  375 ASN cc_start: 0.8084 (m-40) cc_final: 0.7670 (m110)
REVERT: A  377 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7598 (mp0)
REVERT: A  381 THR cc_start: 0.7989 (p) cc_final: 0.7733 (t)
REVERT: A  436 GLN cc_start: 0.7941 (mm110) cc_final: 0.7605 (mp-120)
REVERT: A  541 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7311 (mptt)
REVERT: A  586 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7618 (mt-10)
  outliers start: 13
  outliers final: 5
  residues processed: 57
  average time/residue: 1.1299
  time to fit residues: 67.0846
Evaluate side-chains
  55 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  586 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 350 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.132973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.120023 restraints weight = 4567.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 0.84
r_work: 0.3092 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4491  Z= 0.145
  Angle     :  0.551   6.321   6131  Z= 0.293
  Chirality :  0.041   0.133    688
  Planarity :  0.005   0.053    743
  Dihedral  :  4.305  21.762    605
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.16 %
    Favored  : 86.21 %
  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:  0.92 (0.37), residues: 538
  helix:  1.59 (0.28), residues: 350
  sheet:  None (None), residues: 0
  loop : -1.31 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 553 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.016   0.002   PHE A 409 
 TYR   0.018   0.002   TYR A  84 
 ARG   0.003   0.000   ARG A 301 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00324 (    1)
  link_NAG-ASN         : angle       1.05274 (    3)
  hydrogen bonds       : bond        0.07182 (  250)
  hydrogen bonds       : angle       4.48229 (  723)
  SS BOND              : bond        0.00565 (    1)
  SS BOND              : angle       2.81498 (    2)
  covalent geometry    : bond        0.00291 ( 4489)
  covalent geometry    : angle       0.54860 ( 6126)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.7954 (ptpt) cc_final: 0.7319 (pttt)
REVERT: A  329 PHE cc_start: 0.8013 (m-80) cc_final: 0.7512 (t80)
REVERT: A  375 ASN cc_start: 0.8111 (m-40) cc_final: 0.7747 (m110)
REVERT: A  381 THR cc_start: 0.8053 (p) cc_final: 0.7805 (t)
REVERT: A  436 GLN cc_start: 0.7927 (mm110) cc_final: 0.7528 (mp-120)
REVERT: A  541 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7374 (mptt)
REVERT: A  586 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7694 (mt-10)
  outliers start: 12
  outliers final: 5
  residues processed: 52
  average time/residue: 1.1303
  time to fit residues: 61.4079
Evaluate side-chains
  53 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  586 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 350 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.136594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.123399 restraints weight = 4487.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 0.87
r_work: 0.3131 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4491  Z= 0.117
  Angle     :  0.491   5.791   6131  Z= 0.261
  Chirality :  0.039   0.128    688
  Planarity :  0.005   0.053    743
  Dihedral  :  4.006  21.553    605
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.60 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.26 (0.38), residues: 538
  helix:  1.95 (0.28), residues: 346
  sheet:  None (None), residues: 0
  loop : -1.29 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 280 
 PHE   0.011   0.001   PHE A 409 
 TYR   0.015   0.001   TYR A  84 
 ARG   0.002   0.000   ARG A 301 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00369 (    1)
  link_NAG-ASN         : angle       0.87810 (    3)
  hydrogen bonds       : bond        0.05879 (  250)
  hydrogen bonds       : angle       4.32010 (  723)
  SS BOND              : bond        0.00373 (    1)
  SS BOND              : angle       2.23992 (    2)
  covalent geometry    : bond        0.00220 ( 4489)
  covalent geometry    : angle       0.48925 ( 6126)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.7891 (ptpt) cc_final: 0.7275 (pttt)
REVERT: A  329 PHE cc_start: 0.8006 (m-80) cc_final: 0.7518 (t80)
REVERT: A  375 ASN cc_start: 0.8054 (m-40) cc_final: 0.7622 (m110)
REVERT: A  377 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7540 (mp0)
REVERT: A  381 THR cc_start: 0.7939 (p) cc_final: 0.7715 (t)
REVERT: A  436 GLN cc_start: 0.7924 (mm110) cc_final: 0.7524 (mp-120)
REVERT: A  541 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7270 (mptt)
REVERT: A  586 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8023 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 56
  average time/residue: 1.1915
  time to fit residues: 69.4869
Evaluate side-chains
  55 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  586 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0060
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
A 350 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.135186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.122520 restraints weight = 4513.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 0.81
r_work: 0.3103 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
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      :  0.002   0.030   4491  Z= 0.124
  Angle     :  0.504   6.163   6131  Z= 0.268
  Chirality :  0.040   0.125    688
  Planarity :  0.005   0.054    743
  Dihedral  :  4.038  21.750    605
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.38 %
    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:  1.32 (0.38), residues: 538
  helix:  1.98 (0.28), residues: 347
  sheet:  None (None), residues: 0
  loop : -1.26 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 553 
 HIS   0.003   0.001   HIS A 280 
 PHE   0.013   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.002   0.000   ARG A 301 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00349 (    1)
  link_NAG-ASN         : angle       0.81466 (    3)
  hydrogen bonds       : bond        0.06241 (  250)
  hydrogen bonds       : angle       4.33450 (  723)
  SS BOND              : bond        0.00406 (    1)
  SS BOND              : angle       2.26833 (    2)
  covalent geometry    : bond        0.00240 ( 4489)
  covalent geometry    : angle       0.50265 ( 6126)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.7899 (ptpt) cc_final: 0.7362 (pttp)
REVERT: A  329 PHE cc_start: 0.8009 (m-80) cc_final: 0.7535 (t80)
REVERT: A  375 ASN cc_start: 0.8073 (m-40) cc_final: 0.7652 (m110)
REVERT: A  377 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7471 (mp0)
REVERT: A  381 THR cc_start: 0.7927 (p) cc_final: 0.7705 (t)
REVERT: A  436 GLN cc_start: 0.7910 (mm110) cc_final: 0.7511 (mp-120)
REVERT: A  541 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7278 (mptt)
REVERT: A  586 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8015 (mp0)
  outliers start: 12
  outliers final: 7
  residues processed: 53
  average time/residue: 1.0784
  time to fit residues: 59.6859
Evaluate side-chains
  55 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  586 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0470
   chunk 38 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    0.7478

-------------------------------------------------------------------------------
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 = 0.3373 r_free = 0.3373 target = 0.134256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.121680 restraints weight = 4432.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 0.79
r_work: 0.3113 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4491  Z= 0.129
  Angle     :  0.514   6.301   6131  Z= 0.273
  Chirality :  0.040   0.125    688
  Planarity :  0.005   0.054    743
  Dihedral  :  4.077  21.777    605
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.60 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.53 (0.38), residues: 538
  helix:  2.13 (0.28), residues: 341
  sheet:  None (None), residues: 0
  loop : -1.05 (0.47), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 585 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.014   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.002   0.000   ARG A 301 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00346 (    1)
  link_NAG-ASN         : angle       0.74785 (    3)
  hydrogen bonds       : bond        0.06459 (  250)
  hydrogen bonds       : angle       4.36046 (  723)
  SS BOND              : bond        0.00404 (    1)
  SS BOND              : angle       2.36750 (    2)
  covalent geometry    : bond        0.00251 ( 4489)
  covalent geometry    : angle       0.51192 ( 6126)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.7833 (ptpt) cc_final: 0.7305 (pttp)
REVERT: A  329 PHE cc_start: 0.8001 (m-80) cc_final: 0.7543 (t80)
REVERT: A  375 ASN cc_start: 0.8092 (m-40) cc_final: 0.7659 (m110)
REVERT: A  377 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7484 (mp0)
REVERT: A  381 THR cc_start: 0.7949 (p) cc_final: 0.7724 (t)
REVERT: A  436 GLN cc_start: 0.7887 (mm110) cc_final: 0.7498 (mp-120)
REVERT: A  541 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7283 (mptt)
REVERT: A  586 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7605 (mt-10)
  outliers start: 12
  outliers final: 8
  residues processed: 54
  average time/residue: 1.1345
  time to fit residues: 65.5604
Evaluate side-chains
  57 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  377 GLU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  586 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.133043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.120062 restraints weight = 4522.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 0.83
r_work: 0.3086 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4491  Z= 0.139
  Angle     :  0.534   6.407   6131  Z= 0.284
  Chirality :  0.041   0.130    688
  Planarity :  0.005   0.055    743
  Dihedral  :  4.204  21.780    605
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 11.60 %
    Favored  : 85.56 %
  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:  1.40 (0.38), residues: 538
  helix:  2.02 (0.28), residues: 342
  sheet:  None (None), residues: 0
  loop : -1.11 (0.48), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 585 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.015   0.002   PHE A 409 
 TYR   0.017   0.002   TYR A  84 
 ARG   0.002   0.000   ARG A 587 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00349 (    1)
  link_NAG-ASN         : angle       0.75474 (    3)
  hydrogen bonds       : bond        0.06922 (  250)
  hydrogen bonds       : angle       4.42294 (  723)
  SS BOND              : bond        0.00427 (    1)
  SS BOND              : angle       2.54715 (    2)
  covalent geometry    : bond        0.00276 ( 4489)
  covalent geometry    : angle       0.53165 ( 6126)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.7880 (ptpt) cc_final: 0.7359 (ptmt)
REVERT: A  329 PHE cc_start: 0.8009 (m-80) cc_final: 0.7519 (t80)
REVERT: A  375 ASN cc_start: 0.8099 (m-40) cc_final: 0.7733 (m110)
REVERT: A  381 THR cc_start: 0.8003 (p) cc_final: 0.7750 (t)
REVERT: A  425 GLU cc_start: 0.8786 (tp30) cc_final: 0.8582 (tp30)
REVERT: A  436 GLN cc_start: 0.7883 (mm110) cc_final: 0.7499 (mp-120)
REVERT: A  541 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7356 (mptt)
REVERT: A  586 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7634 (mt-10)
  outliers start: 13
  outliers final: 7
  residues processed: 55
  average time/residue: 1.0519
  time to fit residues: 60.5102
Evaluate side-chains
  54 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  586 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 29 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3327 r_free = 0.3327 target = 0.130465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.118281 restraints weight = 4420.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 0.75
r_work: 0.3020 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4491  Z= 0.165
  Angle     :  0.586   6.728   6131  Z= 0.312
  Chirality :  0.043   0.142    688
  Planarity :  0.005   0.057    743
  Dihedral  :  4.497  22.529    605
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.04 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.28 (0.38), residues: 538
  helix:  1.89 (0.28), residues: 340
  sheet:  None (None), residues: 0
  loop : -1.02 (0.47), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 585 
 HIS   0.005   0.001   HIS A 280 
 PHE   0.019   0.002   PHE A 409 
 TYR   0.018   0.002   TYR A  84 
 ARG   0.004   0.001   ARG A 301 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00361 (    1)
  link_NAG-ASN         : angle       0.78061 (    3)
  hydrogen bonds       : bond        0.07943 (  250)
  hydrogen bonds       : angle       4.56798 (  723)
  SS BOND              : bond        0.00551 (    1)
  SS BOND              : angle       2.96094 (    2)
  covalent geometry    : bond        0.00347 ( 4489)
  covalent geometry    : angle       0.58362 ( 6126)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A  206 LYS cc_start: 0.7966 (ptpt) cc_final: 0.7406 (ptmt)
REVERT: A  329 PHE cc_start: 0.8049 (m-80) cc_final: 0.7478 (t80)
REVERT: A  375 ASN cc_start: 0.8201 (m-40) cc_final: 0.7817 (m110)
REVERT: A  381 THR cc_start: 0.8151 (p) cc_final: 0.7837 (t)
REVERT: A  436 GLN cc_start: 0.7924 (mm110) cc_final: 0.7525 (mp-120)
REVERT: A  541 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7415 (mptt)
REVERT: A  586 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7768 (mt-10)
  outliers start: 10
  outliers final: 7
  residues processed: 56
  average time/residue: 1.0075
  time to fit residues: 59.2538
Evaluate side-chains
  56 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  152 TYR
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  586 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0270
   chunk 37 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.7440

-------------------------------------------------------------------------------
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 = 0.3367 r_free = 0.3367 target = 0.133823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.120450 restraints weight = 4510.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 0.89
r_work: 0.3072 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4491  Z= 0.131
  Angle     :  0.525   6.456   6131  Z= 0.280
  Chirality :  0.040   0.127    688
  Planarity :  0.005   0.057    743
  Dihedral  :  4.199  21.634    605
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.69 %
    Favored  : 85.56 %
  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:  1.46 (0.38), residues: 538
  helix:  2.04 (0.28), residues: 344
  sheet:  None (None), residues: 0
  loop : -1.06 (0.48), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 585 
 HIS   0.003   0.001   HIS A 280 
 PHE   0.013   0.001   PHE A 409 
 TYR   0.017   0.001   TYR A  84 
 ARG   0.002   0.000   ARG A 587 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00400 (    1)
  link_NAG-ASN         : angle       0.68243 (    3)
  hydrogen bonds       : bond        0.06580 (  250)
  hydrogen bonds       : angle       4.41106 (  723)
  SS BOND              : bond        0.00382 (    1)
  SS BOND              : angle       2.47737 (    2)
  covalent geometry    : bond        0.00255 ( 4489)
  covalent geometry    : angle       0.52289 ( 6126)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3209.95 seconds
wall clock time: 56 minutes 3.82 seconds (3363.82 seconds total)