Starting phenix.real_space_refine
on Wed Jun  4 21:36:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ukn_20807/06_2025/6ukn_20807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ukn_20807/06_2025/6ukn_20807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ukn_20807/06_2025/6ukn_20807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ukn_20807/06_2025/6ukn_20807.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ukn_20807/06_2025/6ukn_20807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ukn_20807/06_2025/6ukn_20807.cif"
  }
  resolution = 3.65
  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=   0.000 sd=   1.000
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: 6
    Type Number    sf(0)   Gaussians
     K       1      8.98       5
     S      40      5.16       5
     Cl      1      4.86       5
     C    2689      2.51       5
     N     639      2.21       5
     O     739      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4109
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4029
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4029
          Classifications: {'peptide': 536}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 1, ' CL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.14, per 1000 atoms: 0.76
  Number of scatterers: 4109
  At special positions: 0
  Unit cell: (93.234, 68.22, 94.371, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     K       1     19.00
     Cl      1     17.00
     S      40     16.00
     O     739      8.00
     N     639      7.00
     C    2689      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 163 " - pdb=" SG  CYS A 626 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 352 " 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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 312 "
      " NAG C   1 " - " ASN A 360 "
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 511.5 milliseconds
  

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  970

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 1 sheets defined
      66.8% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 124 through 133
      removed outlier: 3.599A  pdb=" N   LEU A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 140
      removed outlier: 4.286A  pdb=" N   PHE A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 148
    Processing helix  chain 'A' and resid 149 through 177
      removed outlier: 3.852A  pdb=" N   THR A 164 " --> pdb=" O   CYS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 193
      removed outlier: 3.629A  pdb=" N   MET A 188 " --> pdb=" O   GLY A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 227
    Processing helix  chain 'A' and resid 239 through 269
      removed outlier: 4.421A  pdb=" N   ALA A 244 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   LEU A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ASN A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 298
      removed outlier: 3.579A  pdb=" N   VAL A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ASN A 274 " --> pdb=" O   VAL A 270 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   LYS A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   LEU A 278 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   VAL A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 343
    Processing helix  chain 'A' and resid 353 through 359
    Processing helix  chain 'A' and resid 421 through 428
      removed outlier: 4.156A  pdb=" N   GLY A 425 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 431
      No H-bonds generated for 'chain 'A' and resid 429 through 431'
    Processing helix  chain 'A' and resid 440 through 444
      removed outlier: 3.752A  pdb=" N   LEU A 444 " --> pdb=" O   SER A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 477
      Proline residue:  A 452  - end of helix
      removed outlier: 3.942A  pdb=" N   ILE A 456 " --> pdb=" O   PRO A 452 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA A 475 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 477 " --> pdb=" O   PHE A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
      removed outlier: 3.783A  pdb=" N   ARG A 483 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 499
    Processing helix  chain 'A' and resid 504 through 536
      removed outlier: 3.952A  pdb=" N   ILE A 509 " --> pdb=" O   TRP A 505 " (cutoff:3.500A)
      Proline residue:  A 527  - end of helix
      removed outlier: 3.870A  pdb=" N   ASP A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 543
      removed outlier: 4.038A  pdb=" N   GLN A 543 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 570
      removed outlier: 3.842A  pdb=" N   LEU A 559 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU A 560 " --> pdb=" O   TRP A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 602
      removed outlier: 3.696A  pdb=" N   ALA A 578 " --> pdb=" O   LEU A 574 " (cutoff:3.500A)
      Proline residue:  A 579  - end of helix
    Processing helix  chain 'A' and resid 615 through 634
      removed outlier: 4.425A  pdb=" N   SER A 619 " --> pdb=" O   HIS A 615 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE A 620 " --> pdb=" O   TRP A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 652
      removed outlier: 4.034A  pdb=" N   PHE A 640 " --> pdb=" O   TYR A 636 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   TYR A 651 " --> pdb=" O   CYS A 647 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ILE A 652 " --> pdb=" O   ILE A 648 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 309
      removed outlier: 4.046A  pdb=" N   ILE A 305 " --> pdb=" O   GLY A 366 " (cutoff:3.500A)

    240 hydrogen bonds defined for protein.
    711 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: 1.04

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1233
        1.35 -     1.47: 1103
        1.47 -     1.59: 1805
        1.59 -     1.71: 0
        1.71 -     1.84: 60
  Bond restraints: 4201
  Sorted by residual:
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.50e+00
  bond pdb=" C1  BMA B   3 "
       pdb=" C2  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.550 -0.031 2.00e-02 2.50e+03 2.47e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.32e+00
  bond pdb=" CG1 ILE A 221 "
       pdb=" CD1 ILE A 221 "
    ideal  model  delta    sigma   weight residual
    1.513  1.466  0.047 3.90e-02 6.57e+02 1.46e+00
  bond pdb=" C   PHE A 428 "
       pdb=" N   PRO A 429 "
    ideal  model  delta    sigma   weight residual
    1.336  1.349 -0.013 1.08e-02 8.57e+03 1.39e+00
  ... (remaining 4196 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 5477
        1.84 -     3.67: 201
        3.67 -     5.51: 33
        5.51 -     7.34: 11
        7.34 -     9.18: 1
  Bond angle restraints: 5723
  Sorted by residual:
  angle pdb=" C   ASP A 484 "
        pdb=" N   LYS A 485 "
        pdb=" CA  LYS A 485 "
      ideal   model   delta    sigma   weight residual
     121.54  130.72   -9.18 1.91e+00 2.74e-01 2.31e+01
  angle pdb=" C   LYS A 325 "
        pdb=" N   MET A 326 "
        pdb=" CA  MET A 326 "
      ideal   model   delta    sigma   weight residual
     120.82  127.52   -6.70 1.50e+00 4.44e-01 2.00e+01
  angle pdb=" C   PHE A 420 "
        pdb=" N   THR A 421 "
        pdb=" CA  THR A 421 "
      ideal   model   delta    sigma   weight residual
     121.54  127.50   -5.96 1.91e+00 2.74e-01 9.75e+00
  angle pdb=" C   VAL A 400 "
        pdb=" N   SER A 401 "
        pdb=" CA  SER A 401 "
      ideal   model   delta    sigma   weight residual
     122.35  126.42   -4.07 1.46e+00 4.69e-01 7.79e+00
  angle pdb=" C   ALA A 350 "
        pdb=" N   THR A 351 "
        pdb=" CA  THR A 351 "
      ideal   model   delta    sigma   weight residual
     122.46  126.36   -3.90 1.41e+00 5.03e-01 7.64e+00
  ... (remaining 5718 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.88: 2316
       22.88 -    45.75: 147
       45.75 -    68.63: 10
       68.63 -    91.51: 28
       91.51 -   114.38: 16
  Dihedral angle restraints: 2517
    sinusoidal: 991
      harmonic: 1526
  Sorted by residual:
  dihedral pdb=" CA  LYS A 325 "
           pdb=" C   LYS A 325 "
           pdb=" N   MET A 326 "
           pdb=" CA  MET A 326 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.93  -25.07     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  CYS A 626 "
           pdb=" C   CYS A 626 "
           pdb=" N   LEU A 627 "
           pdb=" CA  LEU A 627 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.73   21.27     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  GLN A 327 "
           pdb=" C   GLN A 327 "
           pdb=" N   VAL A 328 "
           pdb=" CA  VAL A 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.14   20.86     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 2514 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 671
       0.113 -    0.226: 26
       0.226 -    0.339: 3
       0.339 -    0.452: 0
       0.452 -    0.564: 1
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" C1  BMA C   3 "
            pdb=" O4  NAG C   2 "
            pdb=" C2  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-02 2.50e+03 1.46e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.56    0.16 2.00e-02 2.50e+03 6.27e+01
  chirality pdb=" C1  BMA B   3 "
            pdb=" O4  NAG B   2 "
            pdb=" C2  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 4.13e+01
  ... (remaining 698 not shown)

  Planarity restraints: 696
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 604 "    0.044 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO A 605 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 605 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 605 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 626 "    0.012 2.00e-02 2.50e+03   2.29e-02 5.25e+00
        pdb=" C   CYS A 626 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   CYS A 626 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A 627 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 428 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO A 429 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 429 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 429 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 693 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.85: 1459
        2.85 -     3.42: 4729
        3.42 -     4.00: 7005
        4.00 -     4.57: 10048
        4.57 -     5.14: 14405
  Nonbonded interactions: 37646
  Sorted by model distance:
  nonbonded pdb=" O   SER A 438 "
            pdb=" OG  SER A 438 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   SER A 511 "
            pdb=" OG1 THR A 515 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O4  BMA B   3 "
            pdb=" O6  BMA B   3 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" OD2 ASP A 415 "
            pdb=" NZ  LYS A 485 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" O   SER A 231 "
            pdb=" OG  SER A 231 "
     model   vdw
     2.407 3.040
  ... (remaining 37641 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.510
  Find NCS groups from input model:        0.050
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
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      :  0.006   0.066   4210  Z= 0.259
  Angle     :  1.138  26.037   5747  Z= 0.517
  Chirality :  0.055   0.564    701
  Planarity :  0.006   0.066    694
  Dihedral  : 20.626 114.383   1538
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  9.53 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.59 (0.33), residues: 534
  helix: -0.93 (0.25), residues: 333
  sheet: -2.49 (1.44), residues: 10
  loop : -3.02 (0.43), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 505 
 HIS   0.004   0.002   HIS A 615 
 PHE   0.016   0.002   PHE A 428 
 TYR   0.011   0.001   TYR A 186 
 ARG   0.001   0.000   ARG A 528 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02339 (    2)
  link_NAG-ASN         : angle      10.86311 (    6)
  link_BETA1-4         : bond        0.06482 (    4)
  link_BETA1-4         : angle      15.15885 (   12)
  hydrogen bonds       : bond        0.14098 (  240)
  hydrogen bonds       : angle       5.36859 (  711)
  SS BOND              : bond        0.00630 (    3)
  SS BOND              : angle       1.91657 (    6)
  covalent geometry    : bond        0.00526 ( 4201)
  covalent geometry    : angle       0.83135 ( 5723)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: A  171 MET cc_start: 0.7574 (ttm) cc_final: 0.6959 (ttm)
REVERT: A  279 VAL cc_start: 0.9342 (t) cc_final: 0.8915 (p)
REVERT: A  435 MET cc_start: 0.8320 (mmt) cc_final: 0.7700 (mmt)
REVERT: A  521 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8676 (tm-30)
REVERT: A  547 HIS cc_start: 0.7428 (m170) cc_final: 0.7073 (m170)
REVERT: A  559 LEU cc_start: 0.8698 (tp) cc_final: 0.8481 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1328
  time to fit residues: 21.1535
Evaluate side-chains
  85 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 130 GLN
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 359 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.122725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.103308 restraints weight = 8185.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.106515 restraints weight = 4123.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.108714 restraints weight = 2592.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4210  Z= 0.172
  Angle     :  0.812  17.571   5747  Z= 0.379
  Chirality :  0.048   0.459    701
  Planarity :  0.005   0.056    694
  Dihedral  : 18.211 100.829    693
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.37 %
    Favored  : 78.37 %
  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: -1.18 (0.36), residues: 534
  helix:  0.38 (0.28), residues: 331
  sheet: -1.94 (1.66), residues: 10
  loop : -2.84 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 505 
 HIS   0.003   0.001   HIS A 615 
 PHE   0.014   0.001   PHE A 428 
 TYR   0.011   0.001   TYR A 186 
 ARG   0.002   0.000   ARG A 603 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01722 (    2)
  link_NAG-ASN         : angle       9.16052 (    6)
  link_BETA1-4         : bond        0.00640 (    4)
  link_BETA1-4         : angle       3.33709 (   12)
  hydrogen bonds       : bond        0.05059 (  240)
  hydrogen bonds       : angle       4.33884 (  711)
  SS BOND              : bond        0.01172 (    3)
  SS BOND              : angle       1.70072 (    6)
  covalent geometry    : bond        0.00396 ( 4201)
  covalent geometry    : angle       0.74024 ( 5723)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8851 (mmm) cc_final: 0.8569 (mmm)
REVERT: A  385 ASP cc_start: 0.8587 (t0) cc_final: 0.8369 (t0)
REVERT: A  521 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8575 (tm-30)
REVERT: A  547 HIS cc_start: 0.7470 (m170) cc_final: 0.7110 (m170)
REVERT: A  583 MET cc_start: 0.7614 (tmm) cc_final: 0.7182 (tmm)
  outliers start: 14
  outliers final: 9
  residues processed: 111
  average time/residue: 0.0969
  time to fit residues: 14.9700
Evaluate side-chains
  98 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   chunk 49 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 44 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.123752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.104015 restraints weight = 8133.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.107241 restraints weight = 4164.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.109477 restraints weight = 2616.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4210  Z= 0.136
  Angle     :  0.760  17.431   5747  Z= 0.346
  Chirality :  0.048   0.480    701
  Planarity :  0.004   0.052    694
  Dihedral  : 15.491  95.060    693
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 20.23 %
    Favored  : 74.42 %
  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: -0.48 (0.37), residues: 534
  helix:  1.08 (0.29), residues: 325
  sheet: -1.46 (1.71), residues: 10
  loop : -2.75 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 
 PHE   0.014   0.001   PHE A 154 
 TYR   0.011   0.001   TYR A 614 
 ARG   0.002   0.000   ARG A 603 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01776 (    2)
  link_NAG-ASN         : angle       8.95190 (    6)
  link_BETA1-4         : bond        0.00731 (    4)
  link_BETA1-4         : angle       3.07516 (   12)
  hydrogen bonds       : bond        0.04673 (  240)
  hydrogen bonds       : angle       3.96181 (  711)
  SS BOND              : bond        0.00638 (    3)
  SS BOND              : angle       1.51709 (    6)
  covalent geometry    : bond        0.00298 ( 4201)
  covalent geometry    : angle       0.68843 ( 5723)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A  171 MET cc_start: 0.8108 (ttp) cc_final: 0.6847 (ttm)
REVERT: A  521 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8597 (tm-30)
REVERT: A  547 HIS cc_start: 0.7489 (m170) cc_final: 0.6984 (m90)
  outliers start: 23
  outliers final: 13
  residues processed: 113
  average time/residue: 0.1155
  time to fit residues: 17.7840
Evaluate side-chains
  103 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  618 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 29 optimal weight:    0.0020
   chunk 7 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.126884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.107622 restraints weight = 8198.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.110655 restraints weight = 4303.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.112704 restraints weight = 2792.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4210  Z= 0.135
  Angle     :  0.755  17.283   5747  Z= 0.345
  Chirality :  0.047   0.485    701
  Planarity :  0.004   0.054    694
  Dihedral  : 14.239  91.740    693
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.63 %
    Favored  : 74.88 %
  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: -0.20 (0.38), residues: 534
  helix:  1.36 (0.30), residues: 325
  sheet: -1.40 (1.73), residues: 10
  loop : -2.75 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 635 
 HIS   0.001   0.001   HIS A 615 
 PHE   0.010   0.001   PHE A 428 
 TYR   0.009   0.001   TYR A 272 
 ARG   0.001   0.000   ARG A 340 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01748 (    2)
  link_NAG-ASN         : angle       8.88381 (    6)
  link_BETA1-4         : bond        0.00695 (    4)
  link_BETA1-4         : angle       2.85439 (   12)
  hydrogen bonds       : bond        0.04479 (  240)
  hydrogen bonds       : angle       3.87955 (  711)
  SS BOND              : bond        0.00945 (    3)
  SS BOND              : angle       1.76535 (    6)
  covalent geometry    : bond        0.00300 ( 4201)
  covalent geometry    : angle       0.68518 ( 5723)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8669 (mmm) cc_final: 0.8385 (mmm)
REVERT: A  385 ASP cc_start: 0.8442 (t0) cc_final: 0.8062 (t0)
REVERT: A  435 MET cc_start: 0.8285 (mmt) cc_final: 0.8021 (mmt)
REVERT: A  521 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8572 (tm-30)
REVERT: A  547 HIS cc_start: 0.7460 (m170) cc_final: 0.6992 (m90)
  outliers start: 15
  outliers final: 10
  residues processed: 110
  average time/residue: 0.1101
  time to fit residues: 16.5656
Evaluate side-chains
  99 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  604 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 15 optimal weight:    0.1980
   chunk 50 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 48 optimal weight:    0.1980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.126621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.107489 restraints weight = 8398.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.110453 restraints weight = 4414.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.112489 restraints weight = 2878.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4210  Z= 0.128
  Angle     :  0.721  17.125   5747  Z= 0.330
  Chirality :  0.047   0.492    701
  Planarity :  0.004   0.051    694
  Dihedral  : 13.113  87.350    693
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 23.49 %
    Favored  : 72.56 %
  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:  0.07 (0.38), residues: 534
  helix:  1.58 (0.30), residues: 326
  sheet: -1.16 (1.76), residues: 10
  loop : -2.69 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 
 PHE   0.011   0.001   PHE A 154 
 TYR   0.009   0.001   TYR A 272 
 ARG   0.001   0.000   ARG A 340 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01728 (    2)
  link_NAG-ASN         : angle       8.81531 (    6)
  link_BETA1-4         : bond        0.00648 (    4)
  link_BETA1-4         : angle       2.42457 (   12)
  hydrogen bonds       : bond        0.04258 (  240)
  hydrogen bonds       : angle       3.74135 (  711)
  SS BOND              : bond        0.00696 (    3)
  SS BOND              : angle       1.76442 (    6)
  covalent geometry    : bond        0.00283 ( 4201)
  covalent geometry    : angle       0.65181 ( 5723)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
REVERT: A  262 MET cc_start: 0.8631 (mmm) cc_final: 0.8365 (mmm)
REVERT: A  520 LEU cc_start: 0.9133 (mt) cc_final: 0.8724 (mt)
REVERT: A  521 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8581 (tm-30)
REVERT: A  547 HIS cc_start: 0.7463 (m170) cc_final: 0.7006 (m90)
  outliers start: 17
  outliers final: 12
  residues processed: 110
  average time/residue: 0.1046
  time to fit residues: 15.9585
Evaluate side-chains
  104 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  618 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 6 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.125705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.106907 restraints weight = 8071.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.109815 restraints weight = 4342.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.111606 restraints weight = 2844.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4210  Z= 0.145
  Angle     :  0.742  17.036   5747  Z= 0.338
  Chirality :  0.047   0.506    701
  Planarity :  0.004   0.052    694
  Dihedral  : 12.261  82.514    693
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 24.65 %
    Favored  : 71.16 %
  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:  0.21 (0.39), residues: 534
  helix:  1.66 (0.30), residues: 327
  sheet: -0.87 (1.84), residues: 10
  loop : -2.60 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 
 PHE   0.012   0.001   PHE A 428 
 TYR   0.007   0.001   TYR A 614 
 ARG   0.001   0.000   ARG A 603 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01643 (    2)
  link_NAG-ASN         : angle       8.84136 (    6)
  link_BETA1-4         : bond        0.00694 (    4)
  link_BETA1-4         : angle       2.22247 (   12)
  hydrogen bonds       : bond        0.04302 (  240)
  hydrogen bonds       : angle       3.78925 (  711)
  SS BOND              : bond        0.00614 (    3)
  SS BOND              : angle       1.70507 (    6)
  covalent geometry    : bond        0.00335 ( 4201)
  covalent geometry    : angle       0.67683 ( 5723)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8605 (mmm) cc_final: 0.8384 (mmm)
REVERT: A  297 LYS cc_start: 0.8389 (mptt) cc_final: 0.7817 (tmtt)
REVERT: A  385 ASP cc_start: 0.8364 (t0) cc_final: 0.8081 (t0)
REVERT: A  520 LEU cc_start: 0.9138 (mt) cc_final: 0.8683 (mt)
REVERT: A  521 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8597 (tm-30)
REVERT: A  547 HIS cc_start: 0.7571 (m170) cc_final: 0.7052 (m90)
  outliers start: 18
  outliers final: 14
  residues processed: 105
  average time/residue: 0.1254
  time to fit residues: 17.8248
Evaluate side-chains
  107 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.127045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.108036 restraints weight = 8055.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.110943 restraints weight = 4363.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.112915 restraints weight = 2883.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4210  Z= 0.131
  Angle     :  0.730  16.990   5747  Z= 0.332
  Chirality :  0.047   0.523    701
  Planarity :  0.004   0.049    694
  Dihedral  : 11.454  78.687    693
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 23.95 %
    Favored  : 71.40 %
  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:  0.30 (0.39), residues: 534
  helix:  1.74 (0.30), residues: 327
  sheet: -0.84 (1.84), residues: 10
  loop : -2.58 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 635 
 HIS   0.001   0.000   HIS A 615 
 PHE   0.011   0.001   PHE A 154 
 TYR   0.006   0.001   TYR A 614 
 ARG   0.001   0.000   ARG A 608 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01674 (    2)
  link_NAG-ASN         : angle       8.82454 (    6)
  link_BETA1-4         : bond        0.00695 (    4)
  link_BETA1-4         : angle       2.22177 (   12)
  hydrogen bonds       : bond        0.04136 (  240)
  hydrogen bonds       : angle       3.68868 (  711)
  SS BOND              : bond        0.00502 (    3)
  SS BOND              : angle       1.62049 (    6)
  covalent geometry    : bond        0.00297 ( 4201)
  covalent geometry    : angle       0.66345 ( 5723)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8580 (mmm) cc_final: 0.8363 (mmm)
REVERT: A  358 GLN cc_start: 0.7542 (tt0) cc_final: 0.7245 (tt0)
REVERT: A  520 LEU cc_start: 0.9157 (mt) cc_final: 0.8732 (mt)
REVERT: A  521 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8608 (tm-30)
REVERT: A  627 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9078 (tt)
  outliers start: 20
  outliers final: 12
  residues processed: 111
  average time/residue: 0.1123
  time to fit residues: 17.5847
Evaluate side-chains
  107 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 46 optimal weight:    0.0970
   chunk 22 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 2 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.127291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.108240 restraints weight = 8048.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.111143 restraints weight = 4324.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.113146 restraints weight = 2851.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4210  Z= 0.131
  Angle     :  0.750  16.982   5747  Z= 0.339
  Chirality :  0.048   0.548    701
  Planarity :  0.004   0.050    694
  Dihedral  : 10.728  74.598    693
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 24.88 %
    Favored  : 70.93 %
  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:  0.40 (0.39), residues: 534
  helix:  1.83 (0.30), residues: 327
  sheet: -0.79 (1.83), residues: 10
  loop : -2.55 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 635 
 HIS   0.000   0.000   HIS A 615 
 PHE   0.011   0.001   PHE A 428 
 TYR   0.006   0.001   TYR A 614 
 ARG   0.002   0.000   ARG A 483 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01494 (    2)
  link_NAG-ASN         : angle       8.82988 (    6)
  link_BETA1-4         : bond        0.00696 (    4)
  link_BETA1-4         : angle       2.21759 (   12)
  hydrogen bonds       : bond        0.04124 (  240)
  hydrogen bonds       : angle       3.69782 (  711)
  SS BOND              : bond        0.00486 (    3)
  SS BOND              : angle       1.59240 (    6)
  covalent geometry    : bond        0.00301 ( 4201)
  covalent geometry    : angle       0.68523 ( 5723)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.635 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8590 (mmm) cc_final: 0.8352 (mmm)
REVERT: A  358 GLN cc_start: 0.7466 (tt0) cc_final: 0.7152 (tt0)
REVERT: A  520 LEU cc_start: 0.9151 (mt) cc_final: 0.8720 (mt)
REVERT: A  521 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8623 (tm-30)
REVERT: A  566 GLU cc_start: 0.8112 (tp30) cc_final: 0.7538 (tp30)
  outliers start: 18
  outliers final: 15
  residues processed: 106
  average time/residue: 0.2121
  time to fit residues: 31.8815
Evaluate side-chains
  108 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 27 optimal weight:    0.0670
   chunk 24 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0270
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.128648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.110094 restraints weight = 7961.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.112943 restraints weight = 4312.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.114873 restraints weight = 2850.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4210  Z= 0.125
  Angle     :  0.766  16.797   5747  Z= 0.341
  Chirality :  0.048   0.551    701
  Planarity :  0.004   0.050    694
  Dihedral  :  9.972  70.347    693
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 27.21 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.47 (0.39), residues: 534
  helix:  1.89 (0.30), residues: 327
  sheet: -0.58 (1.79), residues: 10
  loop : -2.53 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 635 
 HIS   0.000   0.000   HIS A 615 
 PHE   0.008   0.001   PHE A 428 
 TYR   0.007   0.001   TYR A 272 
 ARG   0.001   0.000   ARG A 483 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01588 (    2)
  link_NAG-ASN         : angle       8.86258 (    6)
  link_BETA1-4         : bond        0.00707 (    4)
  link_BETA1-4         : angle       2.27242 (   12)
  hydrogen bonds       : bond        0.03962 (  240)
  hydrogen bonds       : angle       3.64387 (  711)
  SS BOND              : bond        0.00422 (    3)
  SS BOND              : angle       1.59809 (    6)
  covalent geometry    : bond        0.00281 ( 4201)
  covalent geometry    : angle       0.70287 ( 5723)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.571 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8548 (mmm) cc_final: 0.8322 (mmm)
REVERT: A  358 GLN cc_start: 0.7491 (tt0) cc_final: 0.7175 (tt0)
REVERT: A  520 LEU cc_start: 0.9149 (mt) cc_final: 0.8725 (mt)
REVERT: A  521 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8621 (tm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1685
  time to fit residues: 24.9737
Evaluate side-chains
  108 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 1.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0570
   chunk 28 optimal weight:    7.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.135130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.117379 restraints weight = 7753.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.120467 restraints weight = 3857.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.122332 restraints weight = 2402.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4210  Z= 0.133
  Angle     :  0.791  16.972   5747  Z= 0.355
  Chirality :  0.048   0.580    701
  Planarity :  0.004   0.050    694
  Dihedral  :  9.414  66.587    693
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 28.60 %
    Favored  : 68.84 %
  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:  0.48 (0.39), residues: 534
  helix:  1.86 (0.30), residues: 327
  sheet: -0.59 (1.76), residues: 10
  loop : -2.47 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 
 PHE   0.011   0.001   PHE A 428 
 TYR   0.007   0.001   TYR A 272 
 ARG   0.003   0.000   ARG A 117 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01576 (    2)
  link_NAG-ASN         : angle       8.92313 (    6)
  link_BETA1-4         : bond        0.00675 (    4)
  link_BETA1-4         : angle       2.29825 (   12)
  hydrogen bonds       : bond        0.03985 (  240)
  hydrogen bonds       : angle       3.72954 (  711)
  SS BOND              : bond        0.00453 (    3)
  SS BOND              : angle       1.54898 (    6)
  covalent geometry    : bond        0.00310 ( 4201)
  covalent geometry    : angle       0.72874 ( 5723)

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.832 
Fit side-chains
REVERT: A  262 MET cc_start: 0.8566 (mmm) cc_final: 0.8366 (mmm)
REVERT: A  358 GLN cc_start: 0.7441 (tt0) cc_final: 0.7123 (tt0)
REVERT: A  520 LEU cc_start: 0.9155 (mt) cc_final: 0.8723 (mt)
REVERT: A  521 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8602 (tm-30)
  outliers start: 11
  outliers final: 11
  residues processed: 105
  average time/residue: 0.1883
  time to fit residues: 27.7639
Evaluate side-chains
  107 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  292 TYR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  636 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 38 optimal weight:    0.6980
   chunk 42 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.135009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.116874 restraints weight = 7735.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.119896 restraints weight = 3895.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.122043 restraints weight = 2460.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4210  Z= 0.135
  Angle     :  0.795  16.992   5747  Z= 0.356
  Chirality :  0.048   0.591    701
  Planarity :  0.004   0.050    694
  Dihedral  :  8.897  62.802    693
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 28.14 %
    Favored  : 68.37 %
  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:  0.48 (0.39), residues: 534
  helix:  1.85 (0.30), residues: 327
  sheet: -0.40 (1.82), residues: 10
  loop : -2.45 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 635 
 HIS   0.001   0.000   HIS A 615 
 PHE   0.010   0.001   PHE A 428 
 TYR   0.011   0.001   TYR A 272 
 ARG   0.001   0.000   ARG A 252 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01592 (    2)
  link_NAG-ASN         : angle       8.95863 (    6)
  link_BETA1-4         : bond        0.00725 (    4)
  link_BETA1-4         : angle       2.30957 (   12)
  hydrogen bonds       : bond        0.04039 (  240)
  hydrogen bonds       : angle       3.74281 (  711)
  SS BOND              : bond        0.00445 (    3)
  SS BOND              : angle       1.53050 (    6)
  covalent geometry    : bond        0.00316 ( 4201)
  covalent geometry    : angle       0.73239 ( 5723)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1916.00 seconds
wall clock time: 35 minutes 7.24 seconds (2107.24 seconds total)