Starting phenix.real_space_refine
on Thu Jul 24 12:02:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zdq_14666/07_2025/7zdq_14666.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zdq_14666/07_2025/7zdq_14666.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zdq_14666/07_2025/7zdq_14666.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zdq_14666/07_2025/7zdq_14666.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zdq_14666/07_2025/7zdq_14666.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zdq_14666/07_2025/7zdq_14666.cif"
  }
  resolution = 3.2
  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=   0.006
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      33      5.16       5
     C    4010      2.51       5
     N    1037      2.21       5
     O    1184      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6264
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4877
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4998
    Chain: "B"
      Number of atoms: 1345
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 166, 1339
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 8, 'TRANS': 157}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 166, 1339
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 8, 'TRANS': 157}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1370
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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
  Time building chain proxies: 7.04, per 1000 atoms: 1.12
  Number of scatterers: 6264
  At special positions: 0
  Unit cell: (96.025, 98.53, 91.85, 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      33     16.00
     O    1184      8.00
     N    1037      7.00
     C    4010      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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 546 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A  53 "
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1438

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      58.7% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 37
      removed outlier: 3.543A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 53
      removed outlier: 3.827A  pdb=" N   SER A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.566A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.538A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 3.608A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.986A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.692A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.687A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 386
    Processing helix  chain 'A' and resid 400 through 414
      removed outlier: 3.584A  pdb=" N   THR A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.401A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
    Processing helix  chain 'A' and resid 565 through 575
    Processing helix  chain 'A' and resid 581 through 588
      removed outlier: 3.538A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 339 through 343
    Processing helix  chain 'B' and resid 368 through 372
      removed outlier: 4.063A  pdb=" N   ALA B 372 " --> pdb=" O   TYR B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 411
      removed outlier: 4.268A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA B 411 " --> pdb=" O   ARG B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.948A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474
      removed outlier: 3.521A  pdb=" N   TYR B 489 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)

    317 hydrogen bonds defined for protein.
    907 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: 1.71

  Time building geometry restraints manager: 1.85 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: 2010
        1.35 -     1.47: 1677
        1.47 -     1.59: 2701
        1.59 -     1.70: 0
        1.70 -     1.82: 54
  Bond restraints: 6442
  Sorted by residual:
  bond pdb=" C   GLU A 589 "
       pdb=" N   PRO A 590 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 1.36e-02 5.41e+03 2.31e+00
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.08e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.86e+00
  bond pdb=" C1  NAG A 703 "
       pdb=" O5  NAG A 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.71e+00
  bond pdb=" C5  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.33e+00
  ... (remaining 6437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 8459
        1.34 -     2.67: 224
        2.67 -     4.01: 50
        4.01 -     5.34: 16
        5.34 -     6.68: 3
  Bond angle restraints: 8752
  Sorted by residual:
  angle pdb=" N   LEU A  39 "
        pdb=" CA  LEU A  39 "
        pdb=" C   LEU A  39 "
      ideal   model   delta    sigma   weight residual
     113.41  108.45    4.96 1.22e+00 6.72e-01 1.65e+01
  angle pdb=" N   ILE A 259 "
        pdb=" CA  ILE A 259 "
        pdb=" C   ILE A 259 "
      ideal   model   delta    sigma   weight residual
     113.20  109.47    3.73 9.60e-01 1.09e+00 1.51e+01
  angle pdb=" C   PRO A 389 "
        pdb=" N   PHE A 390 "
        pdb=" CA  PHE A 390 "
      ideal   model   delta    sigma   weight residual
     120.82  124.88   -4.06 1.50e+00 4.44e-01 7.34e+00
  angle pdb=" CA  ALA A 614 "
        pdb=" C   ALA A 614 "
        pdb=" N   ASP A 615 "
      ideal   model   delta    sigma   weight residual
     119.26  116.40    2.86 1.14e+00 7.69e-01 6.31e+00
  angle pdb=" C   ALA A 614 "
        pdb=" N   ASP A 615 "
        pdb=" CA  ASP A 615 "
      ideal   model   delta    sigma   weight residual
     121.70  126.14   -4.44 1.80e+00 3.09e-01 6.09e+00
  ... (remaining 8747 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 3432
       18.00 -    36.00: 313
       36.00 -    54.00: 57
       54.00 -    71.99: 18
       71.99 -    89.99: 11
  Dihedral angle restraints: 3831
    sinusoidal: 1587
      harmonic: 2244
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   25.70   67.30     1      1.00e+01 1.00e-02 5.90e+01
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -122.22   36.22     1      1.00e+01 1.00e-02 1.85e+01
  dihedral pdb=" CA  CYS A 344 "
           pdb=" C   CYS A 344 "
           pdb=" N   HIS A 345 "
           pdb=" CA  HIS A 345 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.64   17.36     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 3828 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 644
       0.035 -    0.070: 184
       0.070 -    0.105: 73
       0.105 -    0.140: 14
       0.140 -    0.175: 1
  Chirality restraints: 916
  Sorted by residual:
  chirality pdb=" CB  ILE B 410 "
            pdb=" CA  ILE B 410 "
            pdb=" CG1 ILE B 410 "
            pdb=" CG2 ILE B 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.17 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  TYR A 385 "
            pdb=" N   TYR A 385 "
            pdb=" C   TYR A 385 "
            pdb=" CB  TYR A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.80e-01
  ... (remaining 913 not shown)

  Planarity restraints: 1135
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 345 "   -0.052 5.00e-02 4.00e+02   7.73e-02 9.55e+00
        pdb=" N   PRO A 346 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 346 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 346 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 171 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.41e+00
        pdb=" CD  GLU A 171 "    0.027 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 171 "   -0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 171 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 499 "    0.026 5.00e-02 4.00e+02   3.88e-02 2.40e+00
        pdb=" N   PRO A 500 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1132 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 655
        2.75 -     3.29: 6118
        3.29 -     3.82: 10709
        3.82 -     4.36: 12709
        4.36 -     4.90: 21987
  Nonbonded interactions: 52178
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 439 "
            pdb=" OG  SER B 443 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG  SER A 425 "
            pdb=" OD1 ASP A 427 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG1 THR A 229 "
            pdb=" OH  TYR A 516 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   ASP A 431 "
            pdb=" OG1 THR A 434 "
     model   vdw
     2.277 3.040
  ... (remaining 52173 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.370
  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:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.550
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
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   0.045   6450  Z= 0.134
  Angle     :  0.557   6.676   8771  Z= 0.315
  Chirality :  0.040   0.175    916
  Planarity :  0.004   0.077   1132
  Dihedral  : 15.107  89.992   2378
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.45 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.48 (0.31), residues: 757
  helix:  2.02 (0.27), residues: 394
  sheet:  1.39 (0.85), residues: 39
  loop : -0.37 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.021   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A 381 
 ARG   0.006   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00195 (    3)
  link_NAG-ASN         : angle       1.14455 (    9)
  hydrogen bonds       : bond        0.11812 (  317)
  hydrogen bonds       : angle       5.52982 (  907)
  SS BOND              : bond        0.00327 (    5)
  SS BOND              : angle       1.25207 (   10)
  covalent geometry    : bond        0.00268 ( 6442)
  covalent geometry    : angle       0.55528 ( 8752)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A  483 GLU cc_start: 0.7026 (mp0) cc_final: 0.6688 (mp0)
REVERT: A  568 LEU cc_start: 0.7999 (tt) cc_final: 0.7580 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.2208
  time to fit residues: 25.8313
Evaluate side-chains
  77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.1980
   chunk 56 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   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 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 580 ASN
B 498 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.163150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.136965 restraints weight = 18826.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 3.58
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3426
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3426
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.0739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6450  Z= 0.111
  Angle     :  0.491   5.979   8771  Z= 0.256
  Chirality :  0.040   0.160    916
  Planarity :  0.004   0.053   1132
  Dihedral  :  3.962  26.932    896
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  4.17 %
    Favored  : 95.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.52 (0.31), residues: 757
  helix:  2.05 (0.26), residues: 392
  sheet:  1.10 (0.85), residues: 40
  loop : -0.27 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.020   0.001   PHE A 369 
 TYR   0.026   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00250 (    3)
  link_NAG-ASN         : angle       1.23410 (    9)
  hydrogen bonds       : bond        0.04549 (  317)
  hydrogen bonds       : angle       4.53279 (  907)
  SS BOND              : bond        0.00435 (    5)
  SS BOND              : angle       1.14232 (   10)
  covalent geometry    : bond        0.00238 ( 6442)
  covalent geometry    : angle       0.48842 ( 8752)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A  492 PRO cc_start: 0.7682 (Cg_exo) cc_final: 0.7425 (Cg_endo)
  outliers start: 4
  outliers final: 1
  residues processed: 87
  average time/residue: 0.2069
  time to fit residues: 23.7476
Evaluate side-chains
  76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 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 = 0.3735 r_free = 0.3735 target = 0.160983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.134900 restraints weight = 18668.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 3.47
r_work: 0.3053 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6450  Z= 0.127
  Angle     :  0.505   5.889   8771  Z= 0.264
  Chirality :  0.041   0.139    916
  Planarity :  0.004   0.044   1132
  Dihedral  :  3.876  20.925    896
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  4.61 %
    Favored  : 94.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.43 (0.31), residues: 757
  helix:  1.92 (0.26), residues: 398
  sheet:  0.48 (0.75), residues: 51
  loop : -0.22 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.020   0.001   PHE A 369 
 TYR   0.027   0.001   TYR A 385 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    3)
  link_NAG-ASN         : angle       1.52028 (    9)
  hydrogen bonds       : bond        0.05007 (  317)
  hydrogen bonds       : angle       4.49386 (  907)
  SS BOND              : bond        0.00431 (    5)
  SS BOND              : angle       1.16876 (   10)
  covalent geometry    : bond        0.00282 ( 6442)
  covalent geometry    : angle       0.50166 ( 8752)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A  171 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6568 (mp0)
REVERT: A  492 PRO cc_start: 0.7743 (Cg_exo) cc_final: 0.7458 (Cg_endo)
REVERT: B  420 ASP cc_start: 0.7980 (m-30) cc_final: 0.7610 (m-30)
REVERT: B  449 TYR cc_start: 0.7994 (m-80) cc_final: 0.7667 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.1888
  time to fit residues: 20.2716
Evaluate side-chains
  81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0020
   chunk 62 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 72 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.1992

-------------------------------------------------------------------------------
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 = 0.3733 r_free = 0.3733 target = 0.160970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.133269 restraints weight = 17976.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 3.68
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3379
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3379
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6450  Z= 0.123
  Angle     :  0.496   5.881   8771  Z= 0.259
  Chirality :  0.040   0.128    916
  Planarity :  0.004   0.039   1132
  Dihedral  :  3.844  19.782    896
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  5.95 %
    Favored  : 93.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.31), residues: 757
  helix:  1.91 (0.26), residues: 398
  sheet:  0.36 (0.75), residues: 51
  loop : -0.22 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.019   0.001   PHE A 369 
 TYR   0.025   0.001   TYR A 385 
 ARG   0.004   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00191 (    3)
  link_NAG-ASN         : angle       1.49319 (    9)
  hydrogen bonds       : bond        0.04875 (  317)
  hydrogen bonds       : angle       4.44883 (  907)
  SS BOND              : bond        0.00413 (    5)
  SS BOND              : angle       1.07736 (   10)
  covalent geometry    : bond        0.00273 ( 6442)
  covalent geometry    : angle       0.49283 ( 8752)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.620 
Fit side-chains
REVERT: A  323 MET cc_start: 0.8298 (mmt) cc_final: 0.7698 (mmt)
REVERT: A  408 MET cc_start: 0.8325 (mmt) cc_final: 0.7848 (mmt)
REVERT: A  492 PRO cc_start: 0.7573 (Cg_exo) cc_final: 0.7303 (Cg_endo)
  outliers start: 5
  outliers final: 3
  residues processed: 80
  average time/residue: 0.1866
  time to fit residues: 20.0903
Evaluate side-chains
  79 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 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 = 0.3728 r_free = 0.3728 target = 0.160556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.132243 restraints weight = 10579.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.08
r_work: 0.3201 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6450  Z= 0.124
  Angle     :  0.498   5.878   8771  Z= 0.260
  Chirality :  0.040   0.129    916
  Planarity :  0.004   0.037   1132
  Dihedral  :  3.852  21.152    896
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.55 %
    Favored  : 92.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.31), residues: 757
  helix:  1.88 (0.26), residues: 400
  sheet:  0.30 (0.75), residues: 51
  loop : -0.19 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.019   0.001   PHE A 369 
 TYR   0.025   0.001   TYR A 385 
 ARG   0.005   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00187 (    3)
  link_NAG-ASN         : angle       1.48640 (    9)
  hydrogen bonds       : bond        0.04910 (  317)
  hydrogen bonds       : angle       4.43943 (  907)
  SS BOND              : bond        0.00408 (    5)
  SS BOND              : angle       1.07515 (   10)
  covalent geometry    : bond        0.00279 ( 6442)
  covalent geometry    : angle       0.49498 ( 8752)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  492 PRO cc_start: 0.7737 (Cg_exo) cc_final: 0.7455 (Cg_endo)
REVERT: B  420 ASP cc_start: 0.7972 (m-30) cc_final: 0.7762 (m-30)
  outliers start: 4
  outliers final: 4
  residues processed: 79
  average time/residue: 0.1779
  time to fit residues: 19.1635
Evaluate side-chains
  81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 6 optimal weight:    0.3980
   chunk 67 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0270
   chunk 48 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 401 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.164593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.137095 restraints weight = 18983.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 3.78
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3431
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3431
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6450  Z= 0.097
  Angle     :  0.459   5.834   8771  Z= 0.239
  Chirality :  0.039   0.120    916
  Planarity :  0.003   0.036   1132
  Dihedral  :  3.602  19.169    896
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  6.85 %
    Favored  : 92.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.62 (0.32), residues: 757
  helix:  2.08 (0.26), residues: 400
  sheet:  0.24 (0.74), residues: 51
  loop : -0.08 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.002   0.001   HIS A 374 
 PHE   0.018   0.001   PHE A 369 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00229 (    3)
  link_NAG-ASN         : angle       1.28019 (    9)
  hydrogen bonds       : bond        0.04052 (  317)
  hydrogen bonds       : angle       4.29024 (  907)
  SS BOND              : bond        0.00314 (    5)
  SS BOND              : angle       0.86236 (   10)
  covalent geometry    : bond        0.00201 ( 6442)
  covalent geometry    : angle       0.45640 ( 8752)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A  492 PRO cc_start: 0.7538 (Cg_exo) cc_final: 0.7248 (Cg_endo)
REVERT: A  548 THR cc_start: 0.7888 (m) cc_final: 0.7252 (p)
REVERT: B  420 ASP cc_start: 0.7720 (m-30) cc_final: 0.7440 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 84
  average time/residue: 0.1934
  time to fit residues: 21.5338
Evaluate side-chains
  78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 41 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 58 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3742 r_free = 0.3742 target = 0.161781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.135439 restraints weight = 17894.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.34
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6450  Z= 0.116
  Angle     :  0.481   5.870   8771  Z= 0.252
  Chirality :  0.040   0.128    916
  Planarity :  0.003   0.033   1132
  Dihedral  :  3.700  20.740    896
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  7.44 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.31), residues: 757
  helix:  2.01 (0.26), residues: 400
  sheet:  0.27 (0.75), residues: 51
  loop : -0.14 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.018   0.001   PHE A 369 
 TYR   0.023   0.001   TYR A 385 
 ARG   0.006   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00187 (    3)
  link_NAG-ASN         : angle       1.38204 (    9)
  hydrogen bonds       : bond        0.04661 (  317)
  hydrogen bonds       : angle       4.34553 (  907)
  SS BOND              : bond        0.00367 (    5)
  SS BOND              : angle       0.97385 (   10)
  covalent geometry    : bond        0.00258 ( 6442)
  covalent geometry    : angle       0.47881 ( 8752)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A  202 TYR cc_start: 0.8206 (t80) cc_final: 0.7850 (t80)
REVERT: A  492 PRO cc_start: 0.7542 (Cg_exo) cc_final: 0.7267 (Cg_endo)
REVERT: A  548 THR cc_start: 0.7896 (m) cc_final: 0.7281 (p)
  outliers start: 5
  outliers final: 4
  residues processed: 80
  average time/residue: 0.1751
  time to fit residues: 19.1180
Evaluate side-chains
  80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0270
   overall best weight:    0.7038

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.163606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.136754 restraints weight = 15472.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.92
r_work: 0.3157 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6450  Z= 0.102
  Angle     :  0.467   5.860   8771  Z= 0.243
  Chirality :  0.039   0.121    916
  Planarity :  0.003   0.031   1132
  Dihedral  :  3.624  19.401    896
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  7.59 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.31), residues: 757
  helix:  2.06 (0.26), residues: 400
  sheet:  0.25 (0.74), residues: 51
  loop : -0.09 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.017   0.001   PHE A 369 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    3)
  link_NAG-ASN         : angle       1.29067 (    9)
  hydrogen bonds       : bond        0.04247 (  317)
  hydrogen bonds       : angle       4.32575 (  907)
  SS BOND              : bond        0.00326 (    5)
  SS BOND              : angle       0.90570 (   10)
  covalent geometry    : bond        0.00218 ( 6442)
  covalent geometry    : angle       0.46468 ( 8752)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A  376 MET cc_start: 0.8365 (tpp) cc_final: 0.8034 (tpp)
REVERT: A  492 PRO cc_start: 0.7620 (Cg_exo) cc_final: 0.7342 (Cg_endo)
REVERT: A  548 THR cc_start: 0.7897 (m) cc_final: 0.7270 (p)
REVERT: B  420 ASP cc_start: 0.7727 (m-30) cc_final: 0.7473 (m-30)
REVERT: B  449 TYR cc_start: 0.7887 (m-80) cc_final: 0.7617 (m-80)
  outliers start: 4
  outliers final: 3
  residues processed: 79
  average time/residue: 0.2736
  time to fit residues: 29.6451
Evaluate side-chains
  78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 67 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0870
   chunk 35 optimal weight:    8.9990
   overall best weight:    2.1964

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 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 = 0.3647 r_free = 0.3647 target = 0.153875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.125848 restraints weight = 17235.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 3.75
r_work: 0.3008 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6450  Z= 0.174
  Angle     :  0.556   6.050   8771  Z= 0.290
  Chirality :  0.043   0.150    916
  Planarity :  0.004   0.028   1132
  Dihedral  :  4.107  21.976    896
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  7.44 %
    Favored  : 91.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.20 (0.31), residues: 757
  helix:  1.70 (0.26), residues: 401
  sheet:  0.28 (0.75), residues: 51
  loop : -0.28 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.020   0.002   PHE A 400 
 TYR   0.027   0.002   TYR A 385 
 ARG   0.006   0.001   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00160 (    3)
  link_NAG-ASN         : angle       1.64588 (    9)
  hydrogen bonds       : bond        0.05791 (  317)
  hydrogen bonds       : angle       4.56173 (  907)
  SS BOND              : bond        0.00490 (    5)
  SS BOND              : angle       1.30113 (   10)
  covalent geometry    : bond        0.00409 ( 6442)
  covalent geometry    : angle       0.55206 ( 8752)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.6782 (p0) cc_final: 0.6468 (p0)
REVERT: A  492 PRO cc_start: 0.7779 (Cg_exo) cc_final: 0.7496 (Cg_endo)
REVERT: B  420 ASP cc_start: 0.8017 (m-30) cc_final: 0.7711 (m-30)
REVERT: B  449 TYR cc_start: 0.8109 (m-80) cc_final: 0.7878 (m-80)
  outliers start: 4
  outliers final: 4
  residues processed: 83
  average time/residue: 0.2189
  time to fit residues: 24.5731
Evaluate side-chains
  80 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0030
   chunk 61 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.161809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.135010 restraints weight = 10896.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.79
r_work: 0.3289 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6450  Z= 0.107
  Angle     :  0.490   6.016   8771  Z= 0.253
  Chirality :  0.040   0.122    916
  Planarity :  0.003   0.032   1132
  Dihedral  :  3.835  20.099    896
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  7.44 %
    Favored  : 91.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.43 (0.31), residues: 757
  helix:  1.90 (0.26), residues: 401
  sheet:  0.18 (0.75), residues: 51
  loop : -0.13 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 165 
 HIS   0.002   0.001   HIS A 374 
 PHE   0.017   0.001   PHE A 369 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.007   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00225 (    3)
  link_NAG-ASN         : angle       1.37713 (    9)
  hydrogen bonds       : bond        0.04488 (  317)
  hydrogen bonds       : angle       4.39141 (  907)
  SS BOND              : bond        0.00353 (    5)
  SS BOND              : angle       1.00753 (   10)
  covalent geometry    : bond        0.00225 ( 6442)
  covalent geometry    : angle       0.48707 ( 8752)

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.629 
Fit side-chains
REVERT: A  492 PRO cc_start: 0.7710 (Cg_exo) cc_final: 0.7428 (Cg_endo)
REVERT: A  548 THR cc_start: 0.8037 (m) cc_final: 0.7403 (p)
REVERT: B  420 ASP cc_start: 0.7945 (m-30) cc_final: 0.7703 (m-30)
REVERT: B  449 TYR cc_start: 0.8138 (m-80) cc_final: 0.7741 (m-80)
  outliers start: 4
  outliers final: 4
  residues processed: 81
  average time/residue: 0.1895
  time to fit residues: 20.6080
Evaluate side-chains
  85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  571 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 25 optimal weight:    0.7980
   chunk 62 optimal weight:    0.4980
   chunk 31 optimal weight:    9.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 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 = 0.161092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.134642 restraints weight = 8932.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.93
r_work: 0.3283 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6450  Z= 0.117
  Angle     :  0.500   6.572   8771  Z= 0.258
  Chirality :  0.040   0.127    916
  Planarity :  0.003   0.031   1132
  Dihedral  :  3.808  20.918    896
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  7.44 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.42 (0.31), residues: 757
  helix:  1.89 (0.26), residues: 401
  sheet:  0.19 (0.75), residues: 51
  loop : -0.14 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.018   0.001   PHE A 369 
 TYR   0.023   0.001   TYR A 385 
 ARG   0.006   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00196 (    3)
  link_NAG-ASN         : angle       1.37881 (    9)
  hydrogen bonds       : bond        0.04705 (  317)
  hydrogen bonds       : angle       4.38542 (  907)
  SS BOND              : bond        0.00376 (    5)
  SS BOND              : angle       1.03738 (   10)
  covalent geometry    : bond        0.00259 ( 6442)
  covalent geometry    : angle       0.49702 ( 8752)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3668.41 seconds
wall clock time: 65 minutes 36.81 seconds (3936.81 seconds total)