Starting phenix.real_space_refine
on Wed Jul 23 13:26:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e3b_30978/07_2025/7e3b_30978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e3b_30978/07_2025/7e3b_30978.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e3b_30978/07_2025/7e3b_30978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e3b_30978/07_2025/7e3b_30978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e3b_30978/07_2025/7e3b_30978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e3b_30978/07_2025/7e3b_30978.cif"
  }
  resolution = 4.2
  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=   0.001
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      14      5.16       5
     C    2095      2.51       5
     N     541      2.21       5
     O     649      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3299
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "B"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 941
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "C"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 808
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.25, per 1000 atoms: 0.99
  Number of scatterers: 3299
  At special positions: 0
  Unit cell: (68.481, 85.873, 72.829, 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      14     16.00
     O     649      8.00
     N     541      7.00
     C    2095      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.04

  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 601 " - " ASN A 343 "
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 392.3 milliseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  770

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 9 sheets defined
      11.6% alpha, 29.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.331A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.364A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.136A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'B' and resid 61 through 64
    Processing helix  chain 'B' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.561A  pdb=" N   SER B  35 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 11
    Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11
      removed outlier: 3.918A  pdb=" N   THR C  97 " --> pdb=" O   GLN C  90 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49

    111 hydrogen bonds defined for protein.
    255 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.87

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1049
        1.35 -     1.48: 968
        1.48 -     1.60: 1352
        1.60 -     1.73: 0
        1.73 -     1.85: 16
  Bond restraints: 3385
  Sorted by residual:
  bond pdb=" CB  PHE B  78 "
       pdb=" CG  PHE B  78 "
    ideal  model  delta    sigma   weight residual
    1.502  1.454  0.048 2.30e-02 1.89e+03 4.40e+00
  bond pdb=" N   TRP B 112 "
       pdb=" CA  TRP B 112 "
    ideal  model  delta    sigma   weight residual
    1.457  1.479 -0.022 1.29e-02 6.01e+03 2.88e+00
  bond pdb=" CD2 PHE B  78 "
       pdb=" CE2 PHE B  78 "
    ideal  model  delta    sigma   weight residual
    1.382  1.338  0.044 3.00e-02 1.11e+03 2.14e+00
  bond pdb=" CB  TRP B 112 "
       pdb=" CG  TRP B 112 "
    ideal  model  delta    sigma   weight residual
    1.498  1.453  0.045 3.10e-02 1.04e+03 2.12e+00
  bond pdb=" CB  CYS A 379 "
       pdb=" SG  CYS A 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.854 -0.046 3.30e-02 9.18e+02 1.97e+00
  ... (remaining 3380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 4473
        2.09 -     4.17: 117
        4.17 -     6.26: 17
        6.26 -     8.35: 2
        8.35 -    10.44: 1
  Bond angle restraints: 4610
  Sorted by residual:
  angle pdb=" CA  CYS A 432 "
        pdb=" CB  CYS A 432 "
        pdb=" SG  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     114.40  124.84  -10.44 2.30e+00 1.89e-01 2.06e+01
  angle pdb=" CB  LYS B  13 "
        pdb=" CG  LYS B  13 "
        pdb=" CD  LYS B  13 "
      ideal   model   delta    sigma   weight residual
     111.30  118.65   -7.35 2.30e+00 1.89e-01 1.02e+01
  angle pdb=" C   ILE C  83 "
        pdb=" N   ALA C  84 "
        pdb=" CA  ALA C  84 "
      ideal   model   delta    sigma   weight residual
     122.09  116.48    5.61 1.86e+00 2.89e-01 9.11e+00
  angle pdb=" N   CYS A 432 "
        pdb=" CA  CYS A 432 "
        pdb=" C   CYS A 432 "
      ideal   model   delta    sigma   weight residual
     108.60  112.87   -4.27 1.46e+00 4.69e-01 8.54e+00
  angle pdb=" C   GLY A 431 "
        pdb=" N   CYS A 432 "
        pdb=" CA  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     121.80  116.95    4.85 1.71e+00 3.42e-01 8.04e+00
  ... (remaining 4605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 1814
       17.19 -    34.37: 147
       34.37 -    51.55: 26
       51.55 -    68.74: 7
       68.74 -    85.92: 3
  Dihedral angle restraints: 1997
    sinusoidal: 779
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.09   55.91     1      1.00e+01 1.00e-02 4.22e+01
  dihedral pdb=" CA  CYS A 432 "
           pdb=" C   CYS A 432 "
           pdb=" N   VAL A 433 "
           pdb=" CA  VAL A 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.54  -25.46     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ASP B 110 "
           pdb=" C   ASP B 110 "
           pdb=" N   ILE B 111 "
           pdb=" CA  ILE B 111 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.89  -21.11     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 1994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 280
       0.033 -    0.066: 146
       0.066 -    0.099: 41
       0.099 -    0.132: 23
       0.132 -    0.165: 10
  Chirality restraints: 500
  Sorted by residual:
  chirality pdb=" CA  ILE C  29 "
            pdb=" N   ILE C  29 "
            pdb=" C   ILE C  29 "
            pdb=" CB  ILE C  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.81e-01
  chirality pdb=" CA  CYS A 432 "
            pdb=" N   CYS A 432 "
            pdb=" C   CYS A 432 "
            pdb=" CB  CYS A 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.56e-01
  chirality pdb=" CB  ILE B 111 "
            pdb=" CA  ILE B 111 "
            pdb=" CG1 ILE B 111 "
            pdb=" CG2 ILE B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.92e-01
  ... (remaining 497 not shown)

  Planarity restraints: 595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  34 "   -0.025 2.00e-02 2.50e+03   1.61e-02 6.50e+00
        pdb=" CG  TRP B  34 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  34 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  34 "    0.008 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  34 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  34 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  34 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  34 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B   8 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.63e+00
        pdb=" N   PRO B   9 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B   9 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B   9 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  78 "    0.008 2.00e-02 2.50e+03   1.55e-02 2.40e+00
        pdb=" C   PHE B  78 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   PHE B  78 "    0.010 2.00e-02 2.50e+03
        pdb=" N   SER B  79 "    0.009 2.00e-02 2.50e+03
  ... (remaining 592 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 746
        2.77 -     3.30: 3195
        3.30 -     3.84: 5475
        3.84 -     4.37: 6437
        4.37 -     4.90: 11064
  Nonbonded interactions: 26917
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  98 "
            pdb=" N   ARG B  99 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" NH2 ARG A 346 "
            pdb=" OD2 ASP B  98 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" OD1 ASN A 450 "
            pdb=" OH  TYR B  50 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NH2 ARG A 454 "
            pdb=" O   SER A 469 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" NH1 ARG C  18 "
            pdb=" OG1 THR C  20 "
     model   vdw
     2.296 3.120
  ... (remaining 26912 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             13.950
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.560
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
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   0.048   3392  Z= 0.277
  Angle     :  0.817  10.437   4625  Z= 0.461
  Chirality :  0.049   0.165    500
  Planarity :  0.004   0.041    594
  Dihedral  : 13.333  85.922   1209
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 16.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.04 (0.38), residues: 415
  helix: -3.08 (0.86), residues: 26
  sheet: -1.07 (0.45), residues: 130
  loop : -1.32 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP B  34 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.019   0.002   PHE B  78 
 TYR   0.022   0.002   TYR A 365 
 ARG   0.006   0.001   ARG C  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00075 (    1)
  link_NAG-ASN         : angle       1.27390 (    3)
  hydrogen bonds       : bond        0.17338 (  106)
  hydrogen bonds       : angle       8.91532 (  255)
  SS BOND              : bond        0.00891 (    6)
  SS BOND              : angle       2.23094 (   12)
  covalent geometry    : bond        0.00607 ( 3385)
  covalent geometry    : angle       0.80991 ( 4610)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8499 (t70) cc_final: 0.8014 (p0)
REVERT: B   89 ASP cc_start: 0.9199 (m-30) cc_final: 0.8902 (m-30)
REVERT: B  110 ASP cc_start: 0.8840 (t0) cc_final: 0.8568 (t0)
REVERT: C   83 ILE cc_start: 0.9384 (mt) cc_final: 0.9178 (tt)
REVERT: C   88 CYS cc_start: 0.6457 (p) cc_final: 0.6036 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1704
  time to fit residues: 17.5805
Evaluate side-chains
  76 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0970
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0070
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.071345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.057893 restraints weight = 8673.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.059865 restraints weight = 4980.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.061241 restraints weight = 3438.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3392  Z= 0.141
  Angle     :  0.639  10.389   4625  Z= 0.339
  Chirality :  0.047   0.162    500
  Planarity :  0.004   0.033    594
  Dihedral  :  5.570  30.118    485
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.40), residues: 415
  helix: -2.24 (0.87), residues: 27
  sheet: -0.61 (0.47), residues: 130
  loop : -1.17 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  34 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.015   0.001   PHE B  78 
 TYR   0.020   0.001   TYR B  53 
 ARG   0.003   0.001   ARG B  64 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00123 (    1)
  link_NAG-ASN         : angle       1.02939 (    3)
  hydrogen bonds       : bond        0.03866 (  106)
  hydrogen bonds       : angle       7.24249 (  255)
  SS BOND              : bond        0.00819 (    6)
  SS BOND              : angle       1.95374 (   12)
  covalent geometry    : bond        0.00326 ( 3385)
  covalent geometry    : angle       0.63118 ( 4610)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8492 (t70) cc_final: 0.8030 (p0)
REVERT: B    2 VAL cc_start: 0.9202 (t) cc_final: 0.8976 (t)
REVERT: B   53 TYR cc_start: 0.8654 (p90) cc_final: 0.8165 (p90)
REVERT: B  110 ASP cc_start: 0.8814 (t0) cc_final: 0.8514 (t0)
REVERT: C   24 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8248 (tm-30)
REVERT: C   79 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8621 (mm-40)
REVERT: C   82 ASP cc_start: 0.8821 (m-30) cc_final: 0.8604 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1633
  time to fit residues: 19.8066
Evaluate side-chains
  85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 40 optimal weight:    0.1980
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C  34 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 = 0.2923 r_free = 0.2923 target = 0.071390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.057818 restraints weight = 8500.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.059728 restraints weight = 4935.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.061108 restraints weight = 3433.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3392  Z= 0.187
  Angle     :  0.649  10.744   4625  Z= 0.341
  Chirality :  0.047   0.180    500
  Planarity :  0.004   0.034    594
  Dihedral  :  5.264  27.374    485
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.59 (0.40), residues: 415
  helix: -2.38 (0.82), residues: 27
  sheet: -0.58 (0.48), residues: 132
  loop : -1.16 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  34 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.015   0.001   PHE A 429 
 TYR   0.015   0.001   TYR B  53 
 ARG   0.004   0.001   ARG C  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00064 (    1)
  link_NAG-ASN         : angle       1.16187 (    3)
  hydrogen bonds       : bond        0.03529 (  106)
  hydrogen bonds       : angle       6.87210 (  255)
  SS BOND              : bond        0.00848 (    6)
  SS BOND              : angle       2.03171 (   12)
  covalent geometry    : bond        0.00435 ( 3385)
  covalent geometry    : angle       0.64152 ( 4610)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A  452 LEU cc_start: 0.9494 (mt) cc_final: 0.9246 (mt)
REVERT: A  467 ASP cc_start: 0.8510 (t70) cc_final: 0.8005 (p0)
REVERT: B    2 VAL cc_start: 0.9212 (t) cc_final: 0.8990 (t)
REVERT: B   53 TYR cc_start: 0.8665 (p90) cc_final: 0.8236 (p90)
REVERT: B  110 ASP cc_start: 0.8847 (t0) cc_final: 0.8636 (t0)
REVERT: C   24 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8171 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.2395
  time to fit residues: 28.0133
Evaluate side-chains
  83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 4 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
C  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.072711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.059214 restraints weight = 8492.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.061188 restraints weight = 4972.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.062566 restraints weight = 3458.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3392  Z= 0.139
  Angle     :  0.617  10.610   4625  Z= 0.323
  Chirality :  0.046   0.199    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.990  25.670    485
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.50 (0.40), residues: 415
  helix: -2.30 (0.86), residues: 27
  sheet: -0.50 (0.48), residues: 132
  loop : -1.11 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  34 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.012   0.001   PHE A 429 
 TYR   0.018   0.001   TYR B  52 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00130 (    1)
  link_NAG-ASN         : angle       1.07926 (    3)
  hydrogen bonds       : bond        0.03166 (  106)
  hydrogen bonds       : angle       6.62733 (  255)
  SS BOND              : bond        0.00823 (    6)
  SS BOND              : angle       1.84803 (   12)
  covalent geometry    : bond        0.00326 ( 3385)
  covalent geometry    : angle       0.61020 ( 4610)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  452 LEU cc_start: 0.9512 (mt) cc_final: 0.9297 (mt)
REVERT: A  467 ASP cc_start: 0.8475 (t70) cc_final: 0.7992 (p0)
REVERT: B    2 VAL cc_start: 0.9188 (t) cc_final: 0.8963 (t)
REVERT: B   53 TYR cc_start: 0.8814 (p90) cc_final: 0.8297 (p90)
REVERT: C   24 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8196 (tm-30)
REVERT: C   36 TYR cc_start: 0.8924 (m-80) cc_final: 0.8237 (m-80)
REVERT: C   88 CYS cc_start: 0.5848 (p) cc_final: 0.5636 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1674
  time to fit residues: 19.8910
Evaluate side-chains
  80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 15 optimal weight:    0.4980
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0030
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0980
   chunk 22 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.3990

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

Flipped N/Q/H residues before XYZ refinement:
C  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.073843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.060489 restraints weight = 8455.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.062502 restraints weight = 4927.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.063840 restraints weight = 3399.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3392  Z= 0.130
  Angle     :  0.623  10.211   4625  Z= 0.322
  Chirality :  0.047   0.205    500
  Planarity :  0.004   0.033    594
  Dihedral  :  4.795  23.896    485
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.36 (0.40), residues: 415
  helix: -2.20 (0.90), residues: 27
  sheet: -0.38 (0.49), residues: 132
  loop : -1.03 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  34 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.025   0.001   PHE B  78 
 TYR   0.011   0.001   TYR B  53 
 ARG   0.004   0.001   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00134 (    1)
  link_NAG-ASN         : angle       1.07021 (    3)
  hydrogen bonds       : bond        0.03199 (  106)
  hydrogen bonds       : angle       6.52847 (  255)
  SS BOND              : bond        0.00803 (    6)
  SS BOND              : angle       1.86828 (   12)
  covalent geometry    : bond        0.00304 ( 3385)
  covalent geometry    : angle       0.61586 ( 4610)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A  452 LEU cc_start: 0.9507 (mt) cc_final: 0.9295 (mt)
REVERT: A  467 ASP cc_start: 0.8445 (t70) cc_final: 0.7902 (p0)
REVERT: B   53 TYR cc_start: 0.8645 (p90) cc_final: 0.8240 (p90)
REVERT: C   24 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: C   36 TYR cc_start: 0.8901 (m-10) cc_final: 0.8267 (m-80)
REVERT: C   88 CYS cc_start: 0.5586 (p) cc_final: 0.5305 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2542
  time to fit residues: 31.5694
Evaluate side-chains
  83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    0.2980
   chunk 6 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.2941 r_free = 0.2941 target = 0.072595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.059010 restraints weight = 8786.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.061051 restraints weight = 5020.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.062505 restraints weight = 3438.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3392  Z= 0.167
  Angle     :  0.633  10.163   4625  Z= 0.331
  Chirality :  0.047   0.239    500
  Planarity :  0.004   0.033    594
  Dihedral  :  4.818  22.810    485
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.35 (0.40), residues: 415
  helix: -2.22 (0.91), residues: 27
  sheet: -0.42 (0.48), residues: 132
  loop : -0.99 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 105 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.024   0.002   PHE B  78 
 TYR   0.012   0.001   TYR C  91 
 ARG   0.003   0.001   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00135 (    1)
  link_NAG-ASN         : angle       1.27948 (    3)
  hydrogen bonds       : bond        0.03232 (  106)
  hydrogen bonds       : angle       6.41567 (  255)
  SS BOND              : bond        0.00799 (    6)
  SS BOND              : angle       1.74694 (   12)
  covalent geometry    : bond        0.00392 ( 3385)
  covalent geometry    : angle       0.62734 ( 4610)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A  452 LEU cc_start: 0.9473 (mt) cc_final: 0.9253 (mt)
REVERT: A  467 ASP cc_start: 0.8413 (t70) cc_final: 0.7867 (p0)
REVERT: A  525 CYS cc_start: 0.6579 (m) cc_final: 0.6311 (m)
REVERT: B    2 VAL cc_start: 0.9122 (t) cc_final: 0.8882 (t)
REVERT: B   53 TYR cc_start: 0.8624 (p90) cc_final: 0.8262 (p90)
REVERT: C   24 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: C   36 TYR cc_start: 0.9024 (m-10) cc_final: 0.8292 (m-80)
REVERT: C   88 CYS cc_start: 0.5803 (p) cc_final: 0.5575 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.2452
  time to fit residues: 30.0408
Evaluate side-chains
  86 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN
C  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.071520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.058290 restraints weight = 8572.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.060272 restraints weight = 4976.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.061593 restraints weight = 3447.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   3392  Z= 0.202
  Angle     :  0.685  10.171   4625  Z= 0.352
  Chirality :  0.048   0.245    500
  Planarity :  0.004   0.033    594
  Dihedral  :  4.888  23.583    485
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.47 (0.40), residues: 415
  helix: -2.43 (0.91), residues: 27
  sheet: -0.56 (0.46), residues: 132
  loop : -1.02 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 105 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.020   0.002   PHE B  78 
 TYR   0.023   0.002   TYR B  52 
 ARG   0.004   0.001   ARG C  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       1.49145 (    3)
  hydrogen bonds       : bond        0.03369 (  106)
  hydrogen bonds       : angle       6.38700 (  255)
  SS BOND              : bond        0.00843 (    6)
  SS BOND              : angle       1.85442 (   12)
  covalent geometry    : bond        0.00469 ( 3385)
  covalent geometry    : angle       0.67873 ( 4610)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  467 ASP cc_start: 0.8434 (t70) cc_final: 0.7860 (p0)
REVERT: B    2 VAL cc_start: 0.9140 (t) cc_final: 0.8868 (t)
REVERT: B   53 TYR cc_start: 0.8762 (p90) cc_final: 0.8482 (p90)
REVERT: C   24 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8080 (tm-30)
REVERT: C   36 TYR cc_start: 0.9003 (m-10) cc_final: 0.8416 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1810
  time to fit residues: 20.9196
Evaluate side-chains
  84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 5 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN
** C  34 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 = 0.2934 r_free = 0.2934 target = 0.072043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.058750 restraints weight = 8540.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.060734 restraints weight = 4986.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.062124 restraints weight = 3446.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3392  Z= 0.163
  Angle     :  0.669  10.126   4625  Z= 0.346
  Chirality :  0.048   0.267    500
  Planarity :  0.004   0.033    594
  Dihedral  :  4.874  22.832    485
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.41 (0.39), residues: 415
  helix: -2.30 (0.96), residues: 27
  sheet: -0.46 (0.47), residues: 132
  loop : -1.03 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 105 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.018   0.001   PHE B  78 
 TYR   0.027   0.002   TYR B  52 
 ARG   0.004   0.001   ARG C  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00109 (    1)
  link_NAG-ASN         : angle       1.35093 (    3)
  hydrogen bonds       : bond        0.03289 (  106)
  hydrogen bonds       : angle       6.34446 (  255)
  SS BOND              : bond        0.00799 (    6)
  SS BOND              : angle       1.71954 (   12)
  covalent geometry    : bond        0.00383 ( 3385)
  covalent geometry    : angle       0.66361 ( 4610)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A  452 LEU cc_start: 0.9477 (mt) cc_final: 0.9273 (mt)
REVERT: A  467 ASP cc_start: 0.8422 (t70) cc_final: 0.7859 (p0)
REVERT: B    2 VAL cc_start: 0.9120 (t) cc_final: 0.8848 (t)
REVERT: C   23 CYS cc_start: 0.5436 (t) cc_final: 0.4816 (t)
REVERT: C   24 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8100 (tm-30)
REVERT: C   36 TYR cc_start: 0.8954 (m-10) cc_final: 0.8240 (m-80)
REVERT: C   82 ASP cc_start: 0.8594 (m-30) cc_final: 0.8053 (m-30)
REVERT: C   88 CYS cc_start: 0.5899 (p) cc_final: 0.5533 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1942
  time to fit residues: 22.3116
Evaluate side-chains
  86 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 40 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** C  34 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 = 0.2906 r_free = 0.2906 target = 0.070549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.057095 restraints weight = 8726.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.059014 restraints weight = 5027.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.060406 restraints weight = 3488.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3392  Z= 0.213
  Angle     :  0.704  10.489   4625  Z= 0.361
  Chirality :  0.049   0.274    500
  Planarity :  0.004   0.033    594
  Dihedral  :  4.908  23.753    485
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.50 (0.40), residues: 415
  helix: -2.41 (0.94), residues: 27
  sheet: -0.57 (0.46), residues: 132
  loop : -1.04 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  35 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.018   0.002   PHE B  78 
 TYR   0.026   0.002   TYR B  53 
 ARG   0.003   0.001   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00035 (    1)
  link_NAG-ASN         : angle       1.62450 (    3)
  hydrogen bonds       : bond        0.03424 (  106)
  hydrogen bonds       : angle       6.40064 (  255)
  SS BOND              : bond        0.00860 (    6)
  SS BOND              : angle       1.80171 (   12)
  covalent geometry    : bond        0.00497 ( 3385)
  covalent geometry    : angle       0.69763 ( 4610)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8424 (t70) cc_final: 0.7834 (p0)
REVERT: B    2 VAL cc_start: 0.9099 (t) cc_final: 0.8804 (t)
REVERT: C   23 CYS cc_start: 0.5461 (t) cc_final: 0.4178 (t)
REVERT: C   24 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8141 (tm-30)
REVERT: C   36 TYR cc_start: 0.9051 (m-10) cc_final: 0.8352 (m-80)
REVERT: C   88 CYS cc_start: 0.5982 (p) cc_final: 0.5366 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1536
  time to fit residues: 17.4161
Evaluate side-chains
  84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0570
   chunk 32 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
** C  34 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 = 0.2925 r_free = 0.2925 target = 0.071494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.058330 restraints weight = 8536.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.060222 restraints weight = 4959.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.061565 restraints weight = 3449.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3392  Z= 0.154
  Angle     :  0.684  10.320   4625  Z= 0.348
  Chirality :  0.049   0.271    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.791  22.755    485
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.35 (0.40), residues: 415
  helix: -2.33 (0.95), residues: 27
  sheet: -0.37 (0.48), residues: 132
  loop : -1.01 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.019   0.001   PHE B  78 
 TYR   0.021   0.001   TYR B  53 
 ARG   0.004   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00124 (    1)
  link_NAG-ASN         : angle       1.39767 (    3)
  hydrogen bonds       : bond        0.03184 (  106)
  hydrogen bonds       : angle       6.34734 (  255)
  SS BOND              : bond        0.00819 (    6)
  SS BOND              : angle       1.74431 (   12)
  covalent geometry    : bond        0.00366 ( 3385)
  covalent geometry    : angle       0.67831 ( 4610)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  452 LEU cc_start: 0.9422 (mt) cc_final: 0.9197 (mm)
REVERT: A  467 ASP cc_start: 0.8425 (t70) cc_final: 0.7834 (p0)
REVERT: B    2 VAL cc_start: 0.9074 (t) cc_final: 0.8798 (t)
REVERT: B   53 TYR cc_start: 0.8721 (p90) cc_final: 0.8283 (p90)
REVERT: C   24 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: C   36 TYR cc_start: 0.8926 (m-10) cc_final: 0.8224 (m-80)
REVERT: C   82 ASP cc_start: 0.8841 (m-30) cc_final: 0.7960 (m-30)
REVERT: C   88 CYS cc_start: 0.6038 (p) cc_final: 0.5685 (p)
REVERT: C   93 ASN cc_start: 0.8309 (t0) cc_final: 0.7944 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1553
  time to fit residues: 18.2725
Evaluate side-chains
  84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0000
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.4562

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

Flipped N/Q/H residues before XYZ refinement:
** C  34 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 = 0.2943 r_free = 0.2943 target = 0.072528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.059372 restraints weight = 8604.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.061368 restraints weight = 4955.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.062773 restraints weight = 3389.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3392  Z= 0.145
  Angle     :  0.685  10.070   4625  Z= 0.346
  Chirality :  0.047   0.194    500
  Planarity :  0.004   0.034    594
  Dihedral  :  4.671  22.335    485
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.41), residues: 415
  helix: -2.31 (0.94), residues: 27
  sheet: -0.19 (0.49), residues: 132
  loop : -0.95 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 112 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.020   0.001   PHE B  78 
 TYR   0.021   0.001   TYR B  53 
 ARG   0.004   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00135 (    1)
  link_NAG-ASN         : angle       1.28896 (    3)
  hydrogen bonds       : bond        0.03077 (  106)
  hydrogen bonds       : angle       6.25823 (  255)
  SS BOND              : bond        0.00781 (    6)
  SS BOND              : angle       1.80544 (   12)
  covalent geometry    : bond        0.00346 ( 3385)
  covalent geometry    : angle       0.67938 ( 4610)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2686.65 seconds
wall clock time: 49 minutes 45.16 seconds (2985.16 seconds total)