Starting phenix.real_space_refine
on Wed Jul 23 13:52:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zcf_14629/07_2025/7zcf_14629.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zcf_14629/07_2025/7zcf_14629.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zcf_14629/07_2025/7zcf_14629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zcf_14629/07_2025/7zcf_14629.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zcf_14629/07_2025/7zcf_14629.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zcf_14629/07_2025/7zcf_14629.cif"
  }
  resolution = 4.0
  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=  -0.004 sd=   0.044
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    2107      2.51       5
     N     556      2.21       5
     O     635      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 3312
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1595
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "E"
      Number of atoms: 1703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1703
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 10, 'TRANS': 214}
          Chain breaks: 1
    Chain: "C"
      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: 3.66, per 1000 atoms: 1.11
  Number of scatterers: 3312
  At special positions: 0
  Unit cell: (65.786, 91.567, 90.678, 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     635      8.00
     N     556      7.00
     C    2107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 156 " - pdb=" SG  CYS E 222 " 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 C1301 " - " ASN C 343 "
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 404.6 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 6 sheets defined
      8.5% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.854A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   PHE C 342 " --> pdb=" O   PHE C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 4.228A  pdb=" N   TYR C 369 " --> pdb=" O   TYR C 365 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 365 through 370'
    Processing helix  chain 'C' and resid 386 through 390
      removed outlier: 3.676A  pdb=" N   LEU C 390 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 410
      removed outlier: 3.585A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN C 409 " --> pdb=" O   GLU C 406 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 443
      removed outlier: 3.877A  pdb=" N   SER C 443 " --> pdb=" O   ASN C 440 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 213 through 217
      removed outlier: 3.954A  pdb=" N   PHE E 217 " --> pdb=" O   PRO E 214 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.651A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454
      removed outlier: 3.640A  pdb=" N   GLN C 493 " --> pdb=" O   TYR C 453 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 18 through 20
      removed outlier: 3.639A  pdb=" N   LEU E  80 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   THR E  68 " --> pdb=" O   GLN E  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59
      removed outlier: 5.179A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   TYR E  33 " --> pdb=" O   ASP E  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 139
    Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 188
      removed outlier: 3.778A  pdb=" N   SER E 187 " --> pdb=" O   TYR E 183 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   TRP E 169 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   TYR E 183 " --> pdb=" O   LEU E 167 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   LEU E 167 " --> pdb=" O   TYR E 183 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR E 231 " --> pdb=" O   GLN E 224 " (cutoff:3.500A)

    54 hydrogen bonds defined for protein.
    132 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: 0.74

  Time building geometry restraints manager: 0.92 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: 1057
        1.35 -     1.46: 899
        1.46 -     1.58: 1423
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3395
  Sorted by residual:
  bond pdb=" C   PRO E 174 "
       pdb=" O   PRO E 174 "
    ideal  model  delta    sigma   weight residual
    1.235  1.268 -0.033 1.30e-02 5.92e+03 6.36e+00
  bond pdb=" C   PRO E 174 "
       pdb=" N   GLY E 175 "
    ideal  model  delta    sigma   weight residual
    1.333  1.368 -0.036 1.57e-02 4.06e+03 5.19e+00
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  bond pdb=" C   SER E 228 "
       pdb=" N   PRO E 229 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.64e+00
  bond pdb=" C5  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.13e+00
  ... (remaining 3390 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 4379
        1.33 -     2.66: 180
        2.66 -     4.00: 46
        4.00 -     5.33: 7
        5.33 -     6.66: 2
  Bond angle restraints: 4614
  Sorted by residual:
  angle pdb=" N   SER E 140 "
        pdb=" CA  SER E 140 "
        pdb=" C   SER E 140 "
      ideal   model   delta    sigma   weight residual
     109.81  116.47   -6.66 2.21e+00 2.05e-01 9.08e+00
  angle pdb=" N   GLY C 526 "
        pdb=" CA  GLY C 526 "
        pdb=" C   GLY C 526 "
      ideal   model   delta    sigma   weight residual
     112.34  118.46   -6.12 2.04e+00 2.40e-01 8.99e+00
  angle pdb=" N   GLN E 110 "
        pdb=" CA  GLN E 110 "
        pdb=" C   GLN E 110 "
      ideal   model   delta    sigma   weight residual
     114.04  110.83    3.21 1.24e+00 6.50e-01 6.71e+00
  angle pdb=" O   PRO E 174 "
        pdb=" C   PRO E 174 "
        pdb=" N   GLY E 175 "
      ideal   model   delta    sigma   weight residual
     122.64  126.13   -3.49 1.35e+00 5.49e-01 6.68e+00
  angle pdb=" N   PRO C 337 "
        pdb=" CA  PRO C 337 "
        pdb=" C   PRO C 337 "
      ideal   model   delta    sigma   weight residual
     114.68  112.10    2.58 1.04e+00 9.25e-01 6.13e+00
  ... (remaining 4609 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 1812
       17.95 -    35.91: 160
       35.91 -    53.86: 35
       53.86 -    71.82: 4
       71.82 -    89.77: 4
  Dihedral angle restraints: 2015
    sinusoidal: 790
      harmonic: 1225
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.90   45.10     1      1.00e+01 1.00e-02 2.82e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.62  -44.62     1      1.00e+01 1.00e-02 2.77e+01
  dihedral pdb=" CA  SER E 140 "
           pdb=" C   SER E 140 "
           pdb=" N   PRO E 141 "
           pdb=" CA  PRO E 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.22  -23.78     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 2012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 398
       0.049 -    0.097: 80
       0.097 -    0.146: 19
       0.146 -    0.194: 2
       0.194 -    0.243: 1
  Chirality restraints: 500
  Sorted by residual:
  chirality pdb=" CB  ILE C 468 "
            pdb=" CA  ILE C 468 "
            pdb=" CG1 ILE C 468 "
            pdb=" CG2 ILE C 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  ILE C 472 "
            pdb=" N   ILE C 472 "
            pdb=" C   ILE C 472 "
            pdb=" CB  ILE C 472 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.30e-01
  chirality pdb=" CB  VAL E 116 "
            pdb=" CA  VAL E 116 "
            pdb=" CG1 VAL E 116 "
            pdb=" CG2 VAL E 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.78e-01
  ... (remaining 497 not shown)

  Planarity restraints: 598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 336 "    0.035 5.00e-02 4.00e+02   5.38e-02 4.63e+00
        pdb=" N   PRO C 337 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 337 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 337 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 506 "   -0.021 5.00e-02 4.00e+02   3.14e-02 1.57e+00
        pdb=" N   PRO C 507 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 507 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 507 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 411 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.57e+00
        pdb=" N   PRO C 412 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 412 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 412 "    0.018 5.00e-02 4.00e+02
  ... (remaining 595 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 42
        2.65 -     3.21: 2931
        3.21 -     3.78: 4503
        3.78 -     4.34: 6072
        4.34 -     4.90: 10024
  Nonbonded interactions: 23572
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 354 "
            pdb=" OG  SER C 399 "
     model   vdw
     2.089 3.040
  nonbonded pdb=" O   LEU C 455 "
            pdb=" OH  TYR E  33 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OD1 ASN C 331 "
            pdb=" N   ILE C 332 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OH  TYR C 421 "
            pdb=" O   PRO E  53 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" N   GLN E   3 "
            pdb=" OG  SER E  25 "
     model   vdw
     2.311 3.120
  ... (remaining 23567 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 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:             6.540
  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:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.970
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
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   0.036   3402  Z= 0.143
  Angle     :  0.660   6.658   4629  Z= 0.371
  Chirality :  0.045   0.243    500
  Planarity :  0.005   0.054    597
  Dihedral  : 14.299  89.770   1223
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.76 %
    Favored  : 85.24 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  0.28 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.40), residues: 420
  helix: -4.94 (0.47), residues: 8
  sheet: -0.46 (0.55), residues: 104
  loop : -2.12 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 353 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.015   0.001   PHE C 338 
 TYR   0.012   0.001   TYR C 473 
 ARG   0.002   0.000   ARG E  71 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00241 (    1)
  link_NAG-ASN         : angle       1.22629 (    3)
  hydrogen bonds       : bond        0.18437 (   54)
  hydrogen bonds       : angle       6.93570 (  132)
  SS BOND              : bond        0.00217 (    6)
  SS BOND              : angle       0.93469 (   12)
  covalent geometry    : bond        0.00265 ( 3395)
  covalent geometry    : angle       0.65843 ( 4614)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 71
  average time/residue: 0.1551
  time to fit residues: 13.4095
Evaluate side-chains
  58 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  139 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 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 = 0.3835 r_free = 0.3835 target = 0.161859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.143238 restraints weight = 5705.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.146093 restraints weight = 3621.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.148151 restraints weight = 2606.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3674
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3674 r_free = 0.3674    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3674 r_free = 0.3674    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3674
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3402  Z= 0.205
  Angle     :  0.735   7.544   4629  Z= 0.389
  Chirality :  0.049   0.180    500
  Planarity :  0.005   0.036    597
  Dihedral  :  6.778  50.370    496
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.10 %
    Favored  : 81.90 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 12.57 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.41), residues: 420
  helix: -4.83 (0.55), residues: 8
  sheet: -1.32 (0.49), residues: 123
  loop : -2.03 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP E 169 
 HIS   0.003   0.002   HIS C 519 
 PHE   0.018   0.003   PHE C 342 
 TYR   0.025   0.002   TYR E 183 
 ARG   0.005   0.001   ARG E  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00130 (    1)
  link_NAG-ASN         : angle       0.85520 (    3)
  hydrogen bonds       : bond        0.04280 (   54)
  hydrogen bonds       : angle       6.45695 (  132)
  SS BOND              : bond        0.00624 (    6)
  SS BOND              : angle       1.81430 (   12)
  covalent geometry    : bond        0.00466 ( 3395)
  covalent geometry    : angle       0.73019 ( 4614)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: C  331 ASN cc_start: 0.7045 (OUTLIER) cc_final: 0.6750 (p0)
REVERT: C  425 LEU cc_start: 0.8777 (mt) cc_final: 0.8556 (mt)
REVERT: E  139 GLN cc_start: 0.7454 (pt0) cc_final: 0.7238 (pt0)
  outliers start: 9
  outliers final: 7
  residues processed: 79
  average time/residue: 0.1353
  time to fit residues: 13.3772
Evaluate side-chains
  80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  331 ASN
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0770
   chunk 5 optimal weight:    0.3980
   chunk 13 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0980
   chunk 18 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    0.2980
   overall best weight:    0.2738

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 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 = 0.3928 r_free = 0.3928 target = 0.170270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.151866 restraints weight = 5495.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.154862 restraints weight = 3437.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.157025 restraints weight = 2437.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3755 r_free = 0.3755    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3755 r_free = 0.3755    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3402  Z= 0.118
  Angle     :  0.650   6.341   4629  Z= 0.339
  Chirality :  0.045   0.169    500
  Planarity :  0.005   0.034    597
  Dihedral  :  6.277  52.116    493
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.76 %
    Favored  : 85.24 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.04 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.41), residues: 420
  helix: -4.81 (0.56), residues: 8
  sheet: -1.31 (0.50), residues: 120
  loop : -2.02 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.013   0.001   PHE C 456 
 TYR   0.024   0.001   TYR E 183 
 ARG   0.002   0.000   ARG E  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00177 (    1)
  link_NAG-ASN         : angle       0.96601 (    3)
  hydrogen bonds       : bond        0.03288 (   54)
  hydrogen bonds       : angle       6.09005 (  132)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       1.56658 (   12)
  covalent geometry    : bond        0.00271 ( 3395)
  covalent geometry    : angle       0.64529 ( 4614)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: C  398 ASP cc_start: 0.8019 (m-30) cc_final: 0.7777 (m-30)
REVERT: C  401 VAL cc_start: 0.9395 (OUTLIER) cc_final: 0.9192 (p)
REVERT: C  425 LEU cc_start: 0.8864 (mt) cc_final: 0.8629 (mt)
  outliers start: 11
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1309
  time to fit residues: 12.0228
Evaluate side-chains
  73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    0.0370
   chunk 0 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0010
   chunk 1 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.4864

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.163656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.144816 restraints weight = 5790.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.147819 restraints weight = 3642.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.149888 restraints weight = 2607.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3693 r_free = 0.3693    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3402  Z= 0.147
  Angle     :  0.681   7.006   4629  Z= 0.355
  Chirality :  0.045   0.172    500
  Planarity :  0.004   0.031    597
  Dihedral  :  6.385  51.371    493
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.86 %
    Favored  : 82.14 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 18.16 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.41), residues: 420
  helix: -4.79 (0.57), residues: 8
  sheet: -1.57 (0.48), residues: 124
  loop : -1.96 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.017   0.002   PHE C 456 
 TYR   0.023   0.001   TYR E 183 
 ARG   0.002   0.000   ARG E  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00173 (    1)
  link_NAG-ASN         : angle       0.70649 (    3)
  hydrogen bonds       : bond        0.03476 (   54)
  hydrogen bonds       : angle       6.10821 (  132)
  SS BOND              : bond        0.00547 (    6)
  SS BOND              : angle       1.99257 (   12)
  covalent geometry    : bond        0.00341 ( 3395)
  covalent geometry    : angle       0.67430 ( 4614)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
REVERT: C  450 ASN cc_start: 0.8788 (p0) cc_final: 0.8221 (p0)
REVERT: E  139 GLN cc_start: 0.7171 (pt0) cc_final: 0.6688 (pt0)
REVERT: E  224 GLN cc_start: 0.8715 (pp30) cc_final: 0.8388 (pp30)
  outliers start: 15
  outliers final: 10
  residues processed: 71
  average time/residue: 0.2467
  time to fit residues: 21.1837
Evaluate side-chains
  74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0170
   chunk 24 optimal weight:    0.3980
   chunk 6 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 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 = 0.3826 r_free = 0.3826 target = 0.161331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.142705 restraints weight = 5855.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.145724 restraints weight = 3672.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.147768 restraints weight = 2607.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3626
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3626 r_free = 0.3626    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3626 r_free = 0.3626    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3626
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3402  Z= 0.163
  Angle     :  0.699   7.195   4629  Z= 0.367
  Chirality :  0.046   0.177    500
  Planarity :  0.004   0.031    597
  Dihedral  :  6.540  50.683    493
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.95 %
    Favored  : 84.05 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 18.44 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.41), residues: 420
  helix: -4.80 (0.57), residues: 8
  sheet: -1.57 (0.49), residues: 124
  loop : -2.02 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.011   0.002   PHE C 456 
 TYR   0.018   0.001   TYR C 473 
 ARG   0.003   0.000   ARG E  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00234 (    1)
  link_NAG-ASN         : angle       0.93946 (    3)
  hydrogen bonds       : bond        0.03608 (   54)
  hydrogen bonds       : angle       6.11404 (  132)
  SS BOND              : bond        0.00892 (    6)
  SS BOND              : angle       1.52298 (   12)
  covalent geometry    : bond        0.00379 ( 3395)
  covalent geometry    : angle       0.69570 ( 4614)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: C  450 ASN cc_start: 0.8832 (p0) cc_final: 0.8252 (p0)
REVERT: E  139 GLN cc_start: 0.7303 (pt0) cc_final: 0.6738 (pt0)
REVERT: E  215 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: E  224 GLN cc_start: 0.8659 (pp30) cc_final: 0.8351 (pp30)
  outliers start: 17
  outliers final: 15
  residues processed: 70
  average time/residue: 0.2634
  time to fit residues: 24.4694
Evaluate side-chains
  74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    0.1980
   chunk 34 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 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 = 0.3788 r_free = 0.3788 target = 0.158042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.139476 restraints weight = 5991.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.142437 restraints weight = 3743.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.144493 restraints weight = 2663.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.4284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3402  Z= 0.176
  Angle     :  0.706   7.320   4629  Z= 0.370
  Chirality :  0.046   0.179    500
  Planarity :  0.005   0.032    597
  Dihedral  :  6.590  50.332    493
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.10 %
    Favored  : 81.90 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 19.83 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.41), residues: 420
  helix: -4.71 (0.65), residues: 8
  sheet: -1.67 (0.48), residues: 124
  loop : -2.17 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.010   0.002   PHE C 456 
 TYR   0.023   0.002   TYR E 183 
 ARG   0.003   0.000   ARG E  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00363 (    1)
  link_NAG-ASN         : angle       0.91532 (    3)
  hydrogen bonds       : bond        0.03627 (   54)
  hydrogen bonds       : angle       6.32035 (  132)
  SS BOND              : bond        0.00670 (    6)
  SS BOND              : angle       1.87369 (   12)
  covalent geometry    : bond        0.00411 ( 3395)
  covalent geometry    : angle       0.70009 ( 4614)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.431 
Fit side-chains
REVERT: C  353 TRP cc_start: 0.8835 (p-90) cc_final: 0.8304 (p-90)
REVERT: C  450 ASN cc_start: 0.8944 (p0) cc_final: 0.8395 (p0)
REVERT: E  139 GLN cc_start: 0.7479 (pt0) cc_final: 0.6921 (pt0)
REVERT: E  215 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7470 (tm-30)
REVERT: E  224 GLN cc_start: 0.8719 (pp30) cc_final: 0.8335 (pp30)
  outliers start: 19
  outliers final: 16
  residues processed: 70
  average time/residue: 0.2988
  time to fit residues: 27.1254
Evaluate side-chains
  74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3769 r_free = 0.3769 target = 0.156663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.138090 restraints weight = 5805.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.140935 restraints weight = 3679.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.142978 restraints weight = 2648.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.4616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3402  Z= 0.189
  Angle     :  0.729   7.313   4629  Z= 0.381
  Chirality :  0.046   0.181    500
  Planarity :  0.005   0.031    597
  Dihedral  :  6.676  49.940    493
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.33 %
    Favored  : 81.67 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 20.95 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.41), residues: 420
  helix: -4.70 (0.65), residues: 8
  sheet: -1.74 (0.49), residues: 119
  loop : -2.14 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.009   0.002   PHE E  27 
 TYR   0.018   0.002   TYR C 473 
 ARG   0.003   0.000   ARG E  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00347 (    1)
  link_NAG-ASN         : angle       1.22447 (    3)
  hydrogen bonds       : bond        0.03770 (   54)
  hydrogen bonds       : angle       6.47493 (  132)
  SS BOND              : bond        0.00608 (    6)
  SS BOND              : angle       1.42374 (   12)
  covalent geometry    : bond        0.00440 ( 3395)
  covalent geometry    : angle       0.72554 ( 4614)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.410 
Fit side-chains
REVERT: C  353 TRP cc_start: 0.8885 (p-90) cc_final: 0.8325 (p-90)
REVERT: C  450 ASN cc_start: 0.8889 (p0) cc_final: 0.8325 (p0)
REVERT: E  139 GLN cc_start: 0.7455 (pt0) cc_final: 0.6869 (pt0)
REVERT: E  215 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7469 (tm-30)
  outliers start: 19
  outliers final: 17
  residues processed: 72
  average time/residue: 0.1962
  time to fit residues: 17.1492
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  380 TYR
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  429 PHE
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.0870
   chunk 39 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0050
   chunk 21 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0870
   chunk 19 optimal weight:    0.0570
   overall best weight:    0.1668

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.162207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.144470 restraints weight = 5740.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.147395 restraints weight = 3549.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.149464 restraints weight = 2496.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3402  Z= 0.118
  Angle     :  0.671   6.982   4629  Z= 0.343
  Chirality :  0.045   0.174    500
  Planarity :  0.004   0.032    597
  Dihedral  :  6.100  50.276    493
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.95 %
    Favored  : 84.05 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 23.18 %
    Favored  : 73.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.41), residues: 420
  helix: -4.72 (0.64), residues: 8
  sheet: -1.66 (0.47), residues: 130
  loop : -2.06 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.009   0.001   PHE E  27 
 TYR   0.019   0.001   TYR C 473 
 ARG   0.002   0.000   ARG E  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00367 (    1)
  link_NAG-ASN         : angle       0.88528 (    3)
  hydrogen bonds       : bond        0.02963 (   54)
  hydrogen bonds       : angle       6.01483 (  132)
  SS BOND              : bond        0.00525 (    6)
  SS BOND              : angle       2.05515 (   12)
  covalent geometry    : bond        0.00265 ( 3395)
  covalent geometry    : angle       0.66337 ( 4614)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.8762 (p-90) cc_final: 0.8287 (p-90)
REVERT: C  450 ASN cc_start: 0.8744 (p0) cc_final: 0.8270 (p0)
REVERT: C  492 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8614 (mp)
REVERT: E  139 GLN cc_start: 0.7318 (pt0) cc_final: 0.6848 (pt0)
REVERT: E  215 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7396 (tm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 71
  average time/residue: 0.2172
  time to fit residues: 18.9604
Evaluate side-chains
  73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.0270
   chunk 19 optimal weight:    0.2980
   chunk 14 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0870
   chunk 13 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.3216

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.160817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.143404 restraints weight = 5798.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.146095 restraints weight = 3696.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.148024 restraints weight = 2667.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3672 r_free = 0.3672    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3672 r_free = 0.3672    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3402  Z= 0.128
  Angle     :  0.671   6.954   4629  Z= 0.347
  Chirality :  0.044   0.175    500
  Planarity :  0.004   0.032    597
  Dihedral  :  6.134  51.415    493
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.71 %
    Favored  : 84.29 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 23.74 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.41), residues: 420
  helix: -4.73 (0.62), residues: 8
  sheet: -1.65 (0.49), residues: 119
  loop : -2.01 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.009   0.001   PHE E 217 
 TYR   0.019   0.001   TYR C 473 
 ARG   0.002   0.000   ARG E  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00391 (    1)
  link_NAG-ASN         : angle       0.68956 (    3)
  hydrogen bonds       : bond        0.03083 (   54)
  hydrogen bonds       : angle       5.97610 (  132)
  SS BOND              : bond        0.00589 (    6)
  SS BOND              : angle       1.91141 (   12)
  covalent geometry    : bond        0.00300 ( 3395)
  covalent geometry    : angle       0.66525 ( 4614)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.8805 (p-90) cc_final: 0.8300 (p-90)
REVERT: C  450 ASN cc_start: 0.8771 (p0) cc_final: 0.8292 (p0)
REVERT: E  139 GLN cc_start: 0.7360 (pt0) cc_final: 0.6855 (pt0)
REVERT: E  215 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7443 (tm-30)
  outliers start: 12
  outliers final: 11
  residues processed: 68
  average time/residue: 0.1429
  time to fit residues: 12.3357
Evaluate side-chains
  71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0870
   chunk 41 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3781 r_free = 0.3781 target = 0.157416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.139491 restraints weight = 5754.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.142231 restraints weight = 3641.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.144204 restraints weight = 2622.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3402  Z= 0.171
  Angle     :  0.726   7.166   4629  Z= 0.376
  Chirality :  0.046   0.175    500
  Planarity :  0.004   0.031    597
  Dihedral  :  6.465  51.677    493
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.57 %
    Favored  : 81.43 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 23.74 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.41), residues: 420
  helix: -4.59 (0.75), residues: 8
  sheet: -1.59 (0.50), residues: 119
  loop : -2.08 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.011   0.002   PHE E 205 
 TYR   0.019   0.002   TYR E 183 
 ARG   0.003   0.000   ARG E  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00408 (    1)
  link_NAG-ASN         : angle       0.86234 (    3)
  hydrogen bonds       : bond        0.03546 (   54)
  hydrogen bonds       : angle       6.24211 (  132)
  SS BOND              : bond        0.00591 (    6)
  SS BOND              : angle       1.91319 (   12)
  covalent geometry    : bond        0.00402 ( 3395)
  covalent geometry    : angle       0.72076 ( 4614)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.453 
Fit side-chains
REVERT: C  353 TRP cc_start: 0.8851 (p-90) cc_final: 0.8369 (p-90)
REVERT: C  450 ASN cc_start: 0.8855 (p0) cc_final: 0.8383 (p0)
REVERT: E  215 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7487 (tm-30)
  outliers start: 13
  outliers final: 12
  residues processed: 65
  average time/residue: 0.1485
  time to fit residues: 12.2889
Evaluate side-chains
  70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0470
   chunk 32 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.158084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.140179 restraints weight = 5858.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.143017 restraints weight = 3638.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.145111 restraints weight = 2586.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.4680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3402  Z= 0.153
  Angle     :  0.727   7.172   4629  Z= 0.378
  Chirality :  0.046   0.178    500
  Planarity :  0.004   0.032    597
  Dihedral  :  6.347  51.286    493
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.90 %
    Favored  : 83.10 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 23.18 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.41), residues: 420
  helix: -4.59 (0.75), residues: 8
  sheet: -1.65 (0.50), residues: 117
  loop : -2.04 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 436 
 HIS   0.001   0.000   HIS C 519 
 PHE   0.009   0.001   PHE E  27 
 TYR   0.019   0.001   TYR C 473 
 ARG   0.002   0.000   ARG E  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00429 (    1)
  link_NAG-ASN         : angle       0.86945 (    3)
  hydrogen bonds       : bond        0.03482 (   54)
  hydrogen bonds       : angle       6.24327 (  132)
  SS BOND              : bond        0.00469 (    6)
  SS BOND              : angle       1.25708 (   12)
  covalent geometry    : bond        0.00359 ( 3395)
  covalent geometry    : angle       0.72527 ( 4614)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2294.68 seconds
wall clock time: 42 minutes 52.62 seconds (2572.62 seconds total)