Starting phenix.real_space_refine
on Tue Mar  3 12:35:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y7z_33675/03_2026/7y7z_33675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y7z_33675/03_2026/7y7z_33675.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y7z_33675/03_2026/7y7z_33675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y7z_33675/03_2026/7y7z_33675.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y7z_33675/03_2026/7y7z_33675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y7z_33675/03_2026/7y7z_33675.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.002 sd=   0.130
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: 5
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     Cl      1      4.86       5
     C    2876      2.51       5
     N     661      2.21       5
     O     729      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4303
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4235
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 23, 'TRANS': 508}
    Chain: "A"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 68
          Unusual residues: {' CL': 1, 'NAG': 3, 'TGI': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.19, per 1000 atoms: 0.28
  Number of scatterers: 4303
  At special positions: 0
  Unit cell: (71.445, 74.6925, 96.3425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      36     16.00
     O     729      8.00
     N     661      7.00
     C    2876      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 173 " distance=2.02

  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 702 " - " ASN A 181 "
      " NAG A 703 " - " ASN A 176 "
      " NAG A 704 " - " ASN A 184 "
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 292.0 milliseconds
  

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  972

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 2 sheets defined
      77.4% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 60
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.643A  pdb=" N   VAL A  67 " --> pdb=" O   GLY A  63 " (cutoff:3.500A)
      Proline residue:  A  71  - end of helix
    Processing helix  chain 'A' and resid 79 through 81
      No H-bonds generated for 'chain 'A' and resid 79 through 81'
    Processing helix  chain 'A' and resid 82 through 93
    Processing helix  chain 'A' and resid 94 through 109
    Processing helix  chain 'A' and resid 119 through 122
    Processing helix  chain 'A' and resid 123 through 155
      removed outlier: 3.764A  pdb=" N   LEU A 127 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   PHE A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 197
    Processing helix  chain 'A' and resid 211 through 230
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.946A  pdb=" N   GLY A 237 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 260
      removed outlier: 3.895A  pdb=" N   THR A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 273
      removed outlier: 3.660A  pdb=" N   GLY A 267 " --> pdb=" O   GLY A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 296
      removed outlier: 3.901A  pdb=" N   TRP A 285 " --> pdb=" O   ASP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 310
      removed outlier: 4.157A  pdb=" N   ALA A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 350
      removed outlier: 3.518A  pdb=" N   GLY A 343 " --> pdb=" O   PHE A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 358
    Processing helix  chain 'A' and resid 363 through 374
      removed outlier: 3.511A  pdb=" N   TYR A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      Proline residue:  A 369  - end of helix
    Processing helix  chain 'A' and resid 377 through 412
      removed outlier: 3.668A  pdb=" N   TRP A 381 " --> pdb=" O   ILE A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 417
    Processing helix  chain 'A' and resid 419 through 439
    Processing helix  chain 'A' and resid 442 through 454
      removed outlier: 4.315A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 474
      removed outlier: 3.676A  pdb=" N   PHE A 465 " --> pdb=" O   LEU A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 489
    Processing helix  chain 'A' and resid 493 through 519
      removed outlier: 4.511A  pdb=" N   LYS A 497 " --> pdb=" O   CYS A 493 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   THR A 504 " --> pdb=" O   TRP A 500 " (cutoff:3.500A)
      Proline residue:  A 505  - end of helix
      removed outlier: 3.527A  pdb=" N   GLN A 518 " --> pdb=" O   PHE A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 546
    Processing helix  chain 'A' and resid 546 through 559
      removed outlier: 3.749A  pdb=" N   LEU A 559 " --> pdb=" O   MET A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 572
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174
      removed outlier: 3.565A  pdb=" N   PHE A 174 " --> pdb=" O   THR A 186 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524

    282 hydrogen bonds defined for protein.
    837 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: 0.59

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 648
        1.32 -     1.45: 1359
        1.45 -     1.57: 2375
        1.57 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 4440
  Sorted by residual:
  bond pdb=" C17 TGI A 701 "
       pdb=" O19 TGI A 701 "
    ideal  model  delta    sigma   weight residual
    1.261  1.203  0.058 2.00e-02 2.50e+03 8.37e+00
  bond pdb=" C20 TGI A 701 "
       pdb=" C21 TGI A 701 "
    ideal  model  delta    sigma   weight residual
    1.374  1.430 -0.056 2.00e-02 2.50e+03 7.91e+00
  bond pdb=" C17 TGI A 701 "
       pdb=" O18 TGI A 701 "
    ideal  model  delta    sigma   weight residual
    1.260  1.204  0.056 2.00e-02 2.50e+03 7.80e+00
  bond pdb=" N   VAL A 323 "
       pdb=" CA  VAL A 323 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.030 1.17e-02 7.31e+03 6.73e+00
  bond pdb=" C02 TGI A 701 "
       pdb=" C03 TGI A 701 "
    ideal  model  delta    sigma   weight residual
    1.380  1.423 -0.043 2.00e-02 2.50e+03 4.57e+00
  ... (remaining 4435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 5561
        1.15 -     2.30: 382
        2.30 -     3.45: 71
        3.45 -     4.59: 27
        4.59 -     5.74: 8
  Bond angle restraints: 6049
  Sorted by residual:
  angle pdb=" CA  TYR A  60 "
        pdb=" CB  TYR A  60 "
        pdb=" CG  TYR A  60 "
      ideal   model   delta    sigma   weight residual
     113.90  119.64   -5.74 1.80e+00 3.09e-01 1.02e+01
  angle pdb=" C   ILE A 138 "
        pdb=" N   TYR A 139 "
        pdb=" CA  TYR A 139 "
      ideal   model   delta    sigma   weight residual
     121.14  115.83    5.31 1.75e+00 3.27e-01 9.22e+00
  angle pdb=" CA  VAL A 323 "
        pdb=" C   VAL A 323 "
        pdb=" O   VAL A 323 "
      ideal   model   delta    sigma   weight residual
     121.17  118.28    2.89 1.06e+00 8.90e-01 7.43e+00
  angle pdb=" O   VAL A 323 "
        pdb=" C   VAL A 323 "
        pdb=" N   CYS A 324 "
      ideal   model   delta    sigma   weight residual
     121.91  124.44   -2.53 9.80e-01 1.04e+00 6.67e+00
  angle pdb=" CA  TYR A 139 "
        pdb=" CB  TYR A 139 "
        pdb=" CG  TYR A 139 "
      ideal   model   delta    sigma   weight residual
     113.90  118.46   -4.56 1.80e+00 3.09e-01 6.41e+00
  ... (remaining 6044 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.49: 2287
       20.49 -    40.98: 252
       40.98 -    61.47: 16
       61.47 -    81.96: 2
       81.96 -   102.45: 2
  Dihedral angle restraints: 2559
    sinusoidal: 1027
      harmonic: 1532
  Sorted by residual:
  dihedral pdb=" CA  SER A 456 "
           pdb=" C   SER A 456 "
           pdb=" N   GLY A 457 "
           pdb=" CA  GLY A 457 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.18  -22.82     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  PHE A 339 "
           pdb=" C   PHE A 339 "
           pdb=" N   SER A 340 "
           pdb=" CA  SER A 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.37   21.63     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  TRP A 116 "
           pdb=" C   TRP A 116 "
           pdb=" N   LYS A 117 "
           pdb=" CA  LYS A 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.74   21.26     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 2556 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 512
       0.049 -    0.099: 129
       0.099 -    0.148: 27
       0.148 -    0.198: 2
       0.198 -    0.247: 1
  Chirality restraints: 671
  Sorted by residual:
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 176 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.65    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  VAL A 323 "
            pdb=" N   VAL A 323 "
            pdb=" C   VAL A 323 "
            pdb=" CB  VAL A 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.28e-01
  chirality pdb=" C1  NAG A 702 "
            pdb=" ND2 ASN A 181 "
            pdb=" C2  NAG A 702 "
            pdb=" O5  NAG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.56    0.16 2.00e-01 2.50e+01 6.74e-01
  ... (remaining 668 not shown)

  Planarity restraints: 736
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 184 "    0.219 2.00e-02 2.50e+03   2.83e-01 1.00e+03
        pdb=" CG  ASN A 184 "   -0.091 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 184 "    0.022 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 184 "   -0.483 2.00e-02 2.50e+03
        pdb=" C1  NAG A 704 "    0.333 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C03 TGI A 701 "    0.009 2.00e-02 2.50e+03   1.80e-01 4.05e+02
        pdb=" C07 TGI A 701 "    0.042 2.00e-02 2.50e+03
        pdb=" C08 TGI A 701 "    0.307 2.00e-02 2.50e+03
        pdb=" C09 TGI A 701 "   -0.210 2.00e-02 2.50e+03
        pdb=" C20 TGI A 701 "   -0.148 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 176 "   -0.099 2.00e-02 2.50e+03   1.58e-01 3.11e+02
        pdb=" CG  ASN A 176 "    0.045 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 176 "   -0.055 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 176 "    0.282 2.00e-02 2.50e+03
        pdb=" C1  NAG A 703 "   -0.173 2.00e-02 2.50e+03
  ... (remaining 733 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 38
        2.61 -     3.18: 4047
        3.18 -     3.75: 6585
        3.75 -     4.33: 8993
        4.33 -     4.90: 15408
  Nonbonded interactions: 35071
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 170 "
            pdb=" OE2 GLU A 191 "
     model   vdw
     2.037 3.040
  nonbonded pdb=" O   GLY A 561 "
            pdb=" NH1 ARG A 566 "
     model   vdw
     2.119 3.120
  nonbonded pdb=" O   LEU A 279 "
            pdb=" OG  SER A 280 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   GLY A 114 "
            pdb=" N   LYS A 117 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" OD1 ASN A 181 "
            pdb=" OG1 THR A 183 "
     model   vdw
     2.304 3.040
  ... (remaining 35066 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.030
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
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   0.103   4444  Z= 0.295
  Angle     :  0.862  26.323   6060  Z= 0.421
  Chirality :  0.045   0.247    671
  Planarity :  0.009   0.180    733
  Dihedral  : 15.326 102.447   1584
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.38), residues: 530
  helix:  0.55 (0.27), residues: 395
  sheet:  None (None), residues: 0
  loop : -1.79 (0.56), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  69 
 TYR   0.029   0.002   TYR A  60 
 PHE   0.016   0.002   PHE A 512 
 TRP   0.021   0.002   TRP A 193 
 HIS   0.002   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 ( 4440)
  covalent geometry    : angle       0.71185 ( 6049)
  SS BOND              : bond        0.00608 (    1)
  SS BOND              : angle       2.12729 (    2)
  hydrogen bonds       : bond        0.11080 (  282)
  hydrogen bonds       : angle       5.80034 (  837)
  link_NAG-ASN         : bond        0.09780 (    3)
  link_NAG-ASN         : angle      12.61290 (    9)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8218 (t80) cc_final: 0.7910 (t80)
REVERT: A  314 ASN cc_start: 0.8805 (t0) cc_final: 0.8596 (t0)
REVERT: A  491 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8061 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0739
  time to fit residues: 6.8361
Evaluate side-chains
  69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    0.2980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.172330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.132688 restraints weight = 4537.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 1.94
r_work: 0.3121 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4444  Z= 0.162
  Angle     :  0.711  10.124   6060  Z= 0.348
  Chirality :  0.048   0.338    671
  Planarity :  0.005   0.040    733
  Dihedral  :  7.789  88.015    666
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.73 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.38), residues: 530
  helix:  0.96 (0.27), residues: 397
  sheet:  None (None), residues: 0
  loop : -1.46 (0.55), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 566 
 TYR   0.025   0.002   TYR A  60 
 PHE   0.018   0.002   PHE A 385 
 TRP   0.017   0.001   TRP A 193 
 HIS   0.002   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 4440)
  covalent geometry    : angle       0.68964 ( 6049)
  SS BOND              : bond        0.00320 (    1)
  SS BOND              : angle       1.73706 (    2)
  hydrogen bonds       : bond        0.05828 (  282)
  hydrogen bonds       : angle       4.91516 (  837)
  link_NAG-ASN         : bond        0.01118 (    3)
  link_NAG-ASN         : angle       4.52667 (    9)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 ASN cc_start: 0.8688 (t0) cc_final: 0.8433 (t0)
  outliers start: 4
  outliers final: 3
  residues processed: 64
  average time/residue: 0.0480
  time to fit residues: 4.5041
Evaluate side-chains
  62 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ASN
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4093 r_free = 0.4093 target = 0.171894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.132101 restraints weight = 4503.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 1.94
r_work: 0.3056 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4444  Z= 0.164
  Angle     :  0.667   9.336   6060  Z= 0.327
  Chirality :  0.047   0.366    671
  Planarity :  0.004   0.040    733
  Dihedral  :  7.537  86.954    666
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.39 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.38), residues: 530
  helix:  1.19 (0.27), residues: 392
  sheet:  None (None), residues: 0
  loop : -1.51 (0.53), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 566 
 TYR   0.026   0.002   TYR A  60 
 PHE   0.016   0.001   PHE A  51 
 TRP   0.016   0.001   TRP A 193 
 HIS   0.002   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 4440)
  covalent geometry    : angle       0.64857 ( 6049)
  SS BOND              : bond        0.00271 (    1)
  SS BOND              : angle       1.58629 (    2)
  hydrogen bonds       : bond        0.05772 (  282)
  hydrogen bonds       : angle       4.83177 (  837)
  link_NAG-ASN         : bond        0.01027 (    3)
  link_NAG-ASN         : angle       4.05805 (    9)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A  314 ASN cc_start: 0.8627 (t0) cc_final: 0.8391 (t0)
REVERT: A  345 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7230 (mtp)
  outliers start: 8
  outliers final: 4
  residues processed: 69
  average time/residue: 0.0394
  time to fit residues: 3.9306
Evaluate side-chains
  68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 TYR
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0370
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
A  66 ASN
A 106 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.172950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.133596 restraints weight = 4486.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.93
r_work: 0.3133 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4444  Z= 0.152
  Angle     :  0.639   8.679   6060  Z= 0.314
  Chirality :  0.046   0.374    671
  Planarity :  0.004   0.043    733
  Dihedral  :  7.557  86.228    666
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.72 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.38), residues: 530
  helix:  1.32 (0.27), residues: 393
  sheet:  None (None), residues: 0
  loop : -1.45 (0.53), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 318 
 TYR   0.027   0.001   TYR A  60 
 PHE   0.016   0.001   PHE A 474 
 TRP   0.016   0.001   TRP A 193 
 HIS   0.002   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 4440)
  covalent geometry    : angle       0.62085 ( 6049)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       1.44551 (    2)
  hydrogen bonds       : bond        0.05474 (  282)
  hydrogen bonds       : angle       4.73784 (  837)
  link_NAG-ASN         : bond        0.01132 (    3)
  link_NAG-ASN         : angle       3.97192 (    9)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A  314 ASN cc_start: 0.8664 (t0) cc_final: 0.8437 (t0)
REVERT: A  345 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7324 (mtp)
REVERT: A  355 ASP cc_start: 0.8198 (t0) cc_final: 0.7990 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 72
  average time/residue: 0.0383
  time to fit residues: 4.0810
Evaluate side-chains
  69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 TYR
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    0.0270
   chunk 16 optimal weight:    3.9990
   chunk 51 optimal weight:    0.2980
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0030
   chunk 26 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.4448

-------------------------------------------------------------------------------
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 = 0.4142 r_free = 0.4142 target = 0.176490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.139003 restraints weight = 4483.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.19
r_work: 0.3163 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4444  Z= 0.132
  Angle     :  0.611   8.900   6060  Z= 0.298
  Chirality :  0.045   0.370    671
  Planarity :  0.004   0.042    733
  Dihedral  :  7.767  83.495    666
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 16.81 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.38), residues: 530
  helix:  1.23 (0.26), residues: 409
  sheet:  None (None), residues: 0
  loop : -1.42 (0.57), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 318 
 TYR   0.026   0.001   TYR A  60 
 PHE   0.017   0.001   PHE A 174 
 TRP   0.015   0.001   TRP A 193 
 HIS   0.001   0.000   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4440)
  covalent geometry    : angle       0.59137 ( 6049)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       1.35090 (    2)
  hydrogen bonds       : bond        0.04939 (  282)
  hydrogen bonds       : angle       4.64339 (  837)
  link_NAG-ASN         : bond        0.00994 (    3)
  link_NAG-ASN         : angle       3.98394 (    9)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  185 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6030 (mmm)
REVERT: A  314 ASN cc_start: 0.8620 (t0) cc_final: 0.8404 (t0)
REVERT: A  355 ASP cc_start: 0.8313 (t0) cc_final: 0.8050 (t0)
REVERT: A  416 LEU cc_start: 0.8351 (mt) cc_final: 0.7734 (mp)
  outliers start: 7
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0443
  time to fit residues: 4.3277
Evaluate side-chains
  65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 TYR
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  469 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0060
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.6396

-------------------------------------------------------------------------------
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 = 0.4126 r_free = 0.4126 target = 0.174838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.135359 restraints weight = 4610.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.95
r_work: 0.2899 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4444  Z= 0.144
  Angle     :  0.617   8.981   6060  Z= 0.304
  Chirality :  0.045   0.373    671
  Planarity :  0.004   0.044    733
  Dihedral  :  7.760  82.229    666
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.81 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.38), residues: 530
  helix:  1.31 (0.27), residues: 409
  sheet:  None (None), residues: 0
  loop : -1.38 (0.57), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 318 
 TYR   0.027   0.001   TYR A  60 
 PHE   0.012   0.001   PHE A 174 
 TRP   0.014   0.001   TRP A 230 
 HIS   0.001   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4440)
  covalent geometry    : angle       0.59971 ( 6049)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       1.18000 (    2)
  hydrogen bonds       : bond        0.05216 (  282)
  hydrogen bonds       : angle       4.65196 (  837)
  link_NAG-ASN         : bond        0.00903 (    3)
  link_NAG-ASN         : angle       3.83141 (    9)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6214 (mmp)
REVERT: A  355 ASP cc_start: 0.8287 (t0) cc_final: 0.8051 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 69
  average time/residue: 0.0450
  time to fit residues: 4.5893
Evaluate side-chains
  65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 TYR
Chi-restraints excluded: chain A residue  153 ASN
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  506 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 39 optimal weight:    0.2980
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 6 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 = 0.4129 r_free = 0.4129 target = 0.174961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.135592 restraints weight = 4527.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 1.95
r_work: 0.2905 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4444  Z= 0.143
  Angle     :  0.624   8.500   6060  Z= 0.305
  Chirality :  0.046   0.354    671
  Planarity :  0.004   0.043    733
  Dihedral  :  7.773  83.333    666
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 17.26 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.38), residues: 530
  helix:  1.33 (0.26), residues: 409
  sheet:  None (None), residues: 0
  loop : -1.37 (0.57), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 318 
 TYR   0.027   0.001   TYR A  60 
 PHE   0.010   0.001   PHE A 174 
 TRP   0.014   0.001   TRP A 230 
 HIS   0.001   0.000   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4440)
  covalent geometry    : angle       0.60540 ( 6049)
  SS BOND              : bond        0.00246 (    1)
  SS BOND              : angle       1.23050 (    2)
  hydrogen bonds       : bond        0.05200 (  282)
  hydrogen bonds       : angle       4.62708 (  837)
  link_NAG-ASN         : bond        0.00828 (    3)
  link_NAG-ASN         : angle       3.97634 (    9)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.6443 (tpt) cc_final: 0.5773 (mmt)
REVERT: A  185 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6395 (mmp)
REVERT: A  355 ASP cc_start: 0.8290 (t0) cc_final: 0.8061 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 67
  average time/residue: 0.0398
  time to fit residues: 3.9870
Evaluate side-chains
  66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 TYR
Chi-restraints excluded: chain A residue  153 ASN
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  552 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0770
   chunk 46 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.4141 r_free = 0.4141 target = 0.176103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.136690 restraints weight = 4505.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.95
r_work: 0.2917 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4444  Z= 0.136
  Angle     :  0.611   8.779   6060  Z= 0.300
  Chirality :  0.045   0.366    671
  Planarity :  0.004   0.045    733
  Dihedral  :  7.780  84.429    666
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.58 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.38), residues: 530
  helix:  1.40 (0.26), residues: 410
  sheet:  None (None), residues: 0
  loop : -1.29 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 579 
 TYR   0.027   0.001   TYR A  60 
 PHE   0.010   0.001   PHE A 174 
 TRP   0.015   0.001   TRP A 230 
 HIS   0.001   0.000   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4440)
  covalent geometry    : angle       0.59570 ( 6049)
  SS BOND              : bond        0.00242 (    1)
  SS BOND              : angle       1.17185 (    2)
  hydrogen bonds       : bond        0.05032 (  282)
  hydrogen bonds       : angle       4.59173 (  837)
  link_NAG-ASN         : bond        0.00785 (    3)
  link_NAG-ASN         : angle       3.53471 (    9)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6393 (mmp)
REVERT: A  250 MET cc_start: 0.7308 (mmm) cc_final: 0.7024 (mmm)
REVERT: A  355 ASP cc_start: 0.8327 (t0) cc_final: 0.8076 (t0)
REVERT: A  473 TRP cc_start: 0.8728 (m-10) cc_final: 0.8504 (m-10)
  outliers start: 13
  outliers final: 10
  residues processed: 67
  average time/residue: 0.0431
  time to fit residues: 4.2748
Evaluate side-chains
  68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 TYR
Chi-restraints excluded: chain A residue  153 ASN
Chi-restraints excluded: chain A residue  181 ASN
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  552 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4115 r_free = 0.4115 target = 0.173739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.133831 restraints weight = 4544.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.97
r_work: 0.2878 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4444  Z= 0.159
  Angle     :  0.641   9.380   6060  Z= 0.315
  Chirality :  0.046   0.383    671
  Planarity :  0.004   0.044    733
  Dihedral  :  7.813  83.254    666
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.81 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.38), residues: 530
  helix:  1.37 (0.26), residues: 410
  sheet:  None (None), residues: 0
  loop : -1.27 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  69 
 TYR   0.028   0.001   TYR A  60 
 PHE   0.012   0.001   PHE A 294 
 TRP   0.016   0.001   TRP A 230 
 HIS   0.001   0.000   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4440)
  covalent geometry    : angle       0.62455 ( 6049)
  SS BOND              : bond        0.00298 (    1)
  SS BOND              : angle       1.33760 (    2)
  hydrogen bonds       : bond        0.05449 (  282)
  hydrogen bonds       : angle       4.65942 (  837)
  link_NAG-ASN         : bond        0.00903 (    3)
  link_NAG-ASN         : angle       3.73472 (    9)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5312 (mmt)
REVERT: A  185 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6397 (mmp)
REVERT: A  355 ASP cc_start: 0.8368 (t0) cc_final: 0.8116 (t0)
REVERT: A  473 TRP cc_start: 0.8737 (m-10) cc_final: 0.8502 (m-10)
  outliers start: 14
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0419
  time to fit residues: 4.0611
Evaluate side-chains
  69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 TYR
Chi-restraints excluded: chain A residue  153 ASN
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  552 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 37 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.173968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.134258 restraints weight = 4466.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 1.95
r_work: 0.2884 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   4444  Z= 0.173
  Angle     :  1.196  56.501   6060  Z= 0.661
  Chirality :  0.048   0.579    671
  Planarity :  0.004   0.044    733
  Dihedral  :  7.978  83.506    666
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.03 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.38), residues: 530
  helix:  1.39 (0.26), residues: 410
  sheet:  None (None), residues: 0
  loop : -1.23 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 318 
 TYR   0.027   0.001   TYR A  60 
 PHE   0.011   0.001   PHE A 294 
 TRP   0.013   0.001   TRP A 193 
 HIS   0.001   0.000   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 4440)
  covalent geometry    : angle       1.12989 ( 6049)
  SS BOND              : bond        0.00298 (    1)
  SS BOND              : angle       1.41717 (    2)
  hydrogen bonds       : bond        0.05407 (  282)
  hydrogen bonds       : angle       4.65394 (  837)
  link_NAG-ASN         : bond        0.04064 (    3)
  link_NAG-ASN         : angle      10.20316 (    9)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5803 (tmm)
REVERT: A  185 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6389 (mmp)
REVERT: A  355 ASP cc_start: 0.8363 (t0) cc_final: 0.8110 (t0)
REVERT: A  473 TRP cc_start: 0.8734 (m-10) cc_final: 0.8495 (m-10)
  outliers start: 13
  outliers final: 11
  residues processed: 64
  average time/residue: 0.0441
  time to fit residues: 4.1952
Evaluate side-chains
  69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 TYR
Chi-restraints excluded: chain A residue  153 ASN
Chi-restraints excluded: chain A residue  179 MET
Chi-restraints excluded: chain A residue  181 ASN
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  314 ASN
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  552 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 39 optimal weight:    0.1980
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4129 r_free = 0.4129 target = 0.174936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.135293 restraints weight = 4526.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.96
r_work: 0.2887 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   4444  Z= 0.162
  Angle     :  1.170  52.784   6060  Z= 0.653
  Chirality :  0.050   0.559    671
  Planarity :  0.004   0.044    733
  Dihedral  :  7.946  84.690    666
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.81 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.38), residues: 530
  helix:  1.41 (0.26), residues: 410
  sheet:  None (None), residues: 0
  loop : -1.12 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  69 
 TYR   0.028   0.002   TYR A  60 
 PHE   0.010   0.001   PHE A 339 
 TRP   0.014   0.001   TRP A 193 
 HIS   0.001   0.001   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4440)
  covalent geometry    : angle       1.09652 ( 6049)
  SS BOND              : bond        0.00363 (    1)
  SS BOND              : angle       1.28194 (    2)
  hydrogen bonds       : bond        0.05260 (  282)
  hydrogen bonds       : angle       4.63430 (  837)
  link_NAG-ASN         : bond        0.03100 (    3)
  link_NAG-ASN         : angle      10.61755 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1278.15 seconds
wall clock time: 22 minutes 28.77 seconds (1348.77 seconds total)