Starting phenix.real_space_refine
on Tue Mar  3 12:55:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7the_25893/03_2026/7the_25893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7the_25893/03_2026/7the_25893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7the_25893/03_2026/7the_25893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7the_25893/03_2026/7the_25893.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7the_25893/03_2026/7the_25893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7the_25893/03_2026/7the_25893.cif"
  }
  resolution = 3.87
  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=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1543 atoms to isotropic.
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      17      5.16       5
     C    2098      2.51       5
     N     549      2.21       5
     O     641      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 3305
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1543
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "B"
      Number of atoms: 945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 945
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "C"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 803
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.99, per 1000 atoms: 0.30
  Number of scatterers: 3305
  At special positions: 0
  Unit cell: (65.596, 81.466, 87.814, 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      17     16.00
     O     641      8.00
     N     549      7.00
     C    2098      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  92 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 343 "
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 154.2 milliseconds
  

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  778

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 9 sheets defined
      12.5% alpha, 31.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.981A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
      removed outlier: 4.706A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 4.854A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ALA A 411 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'B' and resid 73 through 75
      No H-bonds generated for 'chain 'B' and resid 73 through 75'
    Processing helix  chain 'C' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 334 through 335
      removed outlier: 7.513A  pdb=" N   ASN A 334 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.975A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.378A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ILE B  34 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   ARG B  50 " --> pdb=" O   ILE B  34 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP B  36 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.378A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   VAL B 102 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.730A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)

    109 hydrogen bonds defined for protein.
    252 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: 0.63

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 928
        1.33 -     1.45: 657
        1.45 -     1.57: 1781
        1.57 -     1.69: 0
        1.69 -     1.81: 22
  Bond restraints: 3388
  Sorted by residual:
  bond pdb=" C5  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.482 -0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" CZ  ARG B  94 "
       pdb=" NH2 ARG B  94 "
    ideal  model  delta    sigma   weight residual
    1.330  1.287  0.043 1.30e-02 5.92e+03 1.10e+01
  bond pdb=" CZ  ARG A 509 "
       pdb=" NH2 ARG A 509 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.04e+01
  bond pdb=" CZ  ARG A 457 "
       pdb=" NH2 ARG A 457 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" CZ  ARG A 357 "
       pdb=" NH2 ARG A 357 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 1.02e+01
  ... (remaining 3383 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 3171
        1.82 -     3.63: 1161
        3.63 -     5.45: 247
        5.45 -     7.26: 22
        7.26 -     9.08: 4
  Bond angle restraints: 4605
  Sorted by residual:
  angle pdb=" CA  PHE A 347 "
        pdb=" CB  PHE A 347 "
        pdb=" CG  PHE A 347 "
      ideal   model   delta    sigma   weight residual
     113.80  119.35   -5.55 1.00e+00 1.00e+00 3.08e+01
  angle pdb=" N   CYS A 361 "
        pdb=" CA  CYS A 361 "
        pdb=" C   CYS A 361 "
      ideal   model   delta    sigma   weight residual
     108.79  117.19   -8.40 1.53e+00 4.27e-01 3.01e+01
  angle pdb=" C   THR A 393 "
        pdb=" N   ASN A 394 "
        pdb=" CA  ASN A 394 "
      ideal   model   delta    sigma   weight residual
     121.75  130.83   -9.08 1.73e+00 3.34e-01 2.75e+01
  angle pdb=" CA  ASP A 405 "
        pdb=" CB  ASP A 405 "
        pdb=" CG  ASP A 405 "
      ideal   model   delta    sigma   weight residual
     112.60  117.25   -4.65 1.00e+00 1.00e+00 2.16e+01
  angle pdb=" CA  ASP C  70 "
        pdb=" CB  ASP C  70 "
        pdb=" CG  ASP C  70 "
      ideal   model   delta    sigma   weight residual
     112.60  117.16   -4.56 1.00e+00 1.00e+00 2.08e+01
  ... (remaining 4600 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 1841
       16.95 -    33.89: 139
       33.89 -    50.84: 30
       50.84 -    67.79: 8
       67.79 -    84.73: 4
  Dihedral angle restraints: 2022
    sinusoidal: 794
      harmonic: 1228
  Sorted by residual:
  dihedral pdb=" CA  ARG B  83 "
           pdb=" C   ARG B  83 "
           pdb=" N   SER B  84 "
           pdb=" CA  SER B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.24   28.76     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  TYR B  32 "
           pdb=" C   TYR B  32 "
           pdb=" N   ALA B  33 "
           pdb=" CA  ALA B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.82   28.18     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  TYR B  91 "
           pdb=" C   TYR B  91 "
           pdb=" N   CYS B  92 "
           pdb=" CA  CYS B  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.36   27.64     0      5.00e+00 4.00e-02 3.06e+01
  ... (remaining 2019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 270
       0.076 -    0.152: 164
       0.152 -    0.228: 49
       0.228 -    0.303: 10
       0.303 -    0.379: 6
  Chirality restraints: 499
  Sorted by residual:
  chirality pdb=" CA  ALA A 520 "
            pdb=" N   ALA A 520 "
            pdb=" C   ALA A 520 "
            pdb=" CB  ALA A 520 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.11    0.38 2.00e-01 2.50e+01 3.60e+00
  chirality pdb=" CA  ARG B  83 "
            pdb=" N   ARG B  83 "
            pdb=" C   ARG B  83 "
            pdb=" CB  ARG B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" CA  LEU A 455 "
            pdb=" N   LEU A 455 "
            pdb=" C   LEU A 455 "
            pdb=" CB  LEU A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.86e+00
  ... (remaining 496 not shown)

  Planarity restraints: 595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  47 "   -0.113 2.00e-02 2.50e+03   5.99e-02 8.96e+01
        pdb=" CG  TRP B  47 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  47 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  47 "    0.069 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  47 "    0.035 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  47 "    0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  47 "    0.087 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  47 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  47 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  47 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 103 "    0.104 2.00e-02 2.50e+03   5.15e-02 6.64e+01
        pdb=" CG  TRP B 103 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 103 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 103 "   -0.039 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 103 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 103 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 103 "   -0.070 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 103 "    0.056 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 103 "   -0.024 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 103 "    0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 351 "    0.102 2.00e-02 2.50e+03   5.49e-02 6.03e+01
        pdb=" CG  TYR A 351 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 351 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 351 "   -0.039 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 351 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 351 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 351 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 351 "    0.085 2.00e-02 2.50e+03
  ... (remaining 592 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 1818
        3.02 -     3.49: 3232
        3.49 -     3.96: 5382
        3.96 -     4.43: 5919
        4.43 -     4.90: 9826
  Nonbonded interactions: 26177
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 442 "
            pdb=" OH  TYR A 451 "
     model   vdw
     2.548 3.040
  nonbonded pdb=" OD1 ASP A 467 "
            pdb=" OG  SER A 469 "
     model   vdw
     2.565 3.040
  nonbonded pdb=" OE2 GLU A 484 "
            pdb=" OH  TYR B  95 "
     model   vdw
     2.566 3.040
  nonbonded pdb=" OH  TYR B 100B"
            pdb=" OD1 ASN C  34 "
     model   vdw
     2.569 3.040
  nonbonded pdb=" OE2 GLU A 406 "
            pdb=" OH  TYR A 495 "
     model   vdw
     2.588 3.040
  ... (remaining 26172 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.110
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
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      :  0.013   0.069   3395  Z= 0.746
  Angle     :  1.878   9.080   4620  Z= 1.233
  Chirality :  0.106   0.379    499
  Planarity :  0.015   0.104    594
  Dihedral  : 13.764  84.731   1226
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 0.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -2.01 (0.39), residues: 417
  helix: -4.02 (0.48), residues: 40
  sheet:  0.21 (0.50), residues: 117
  loop : -1.70 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG A 346 
 TYR   0.102   0.022   TYR A 351 
 PHE   0.062   0.013   PHE B  54 
 TRP   0.113   0.029   TRP B  47 
 HIS   0.007   0.004   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.01303 ( 3388)
  covalent geometry    : angle       1.87726 ( 4605)
  SS BOND              : bond        0.01072 (    6)
  SS BOND              : angle       1.28223 (   12)
  hydrogen bonds       : bond        0.17838 (  107)
  hydrogen bonds       : angle       8.01727 (  252)
  link_NAG-ASN         : bond        0.01889 (    1)
  link_NAG-ASN         : angle       4.19601 (    3)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.7767 (p-90) cc_final: 0.7518 (p-90)
REVERT: A  484 GLU cc_start: 0.8295 (pm20) cc_final: 0.7880 (pm20)
REVERT: A  493 GLN cc_start: 0.8765 (tt0) cc_final: 0.8363 (tt0)
REVERT: A  506 GLN cc_start: 0.7602 (mt0) cc_final: 0.7191 (mt0)
REVERT: B   36 TRP cc_start: 0.9068 (m100) cc_final: 0.8251 (m-10)
REVERT: B   48 MET cc_start: 0.8169 (mtp) cc_final: 0.7521 (mtm)
REVERT: B   56 ILE cc_start: 0.8594 (mt) cc_final: 0.8363 (tt)
REVERT: B  105 GLN cc_start: 0.8720 (tt0) cc_final: 0.8165 (pt0)
REVERT: C   34 ASN cc_start: 0.8908 (m-40) cc_final: 0.7510 (m-40)
REVERT: C   89 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7011 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0924
  time to fit residues: 13.6220
Evaluate side-chains
  91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 501 ASN
B  58 ASN
B  61 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.115503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.103063 restraints weight = 8872.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.105977 restraints weight = 4610.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.107897 restraints weight = 2844.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.109179 restraints weight = 1966.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.110051 restraints weight = 1490.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3395  Z= 0.162
  Angle     :  0.716   6.130   4620  Z= 0.387
  Chirality :  0.047   0.167    499
  Planarity :  0.005   0.035    594
  Dihedral  :  7.471  56.070    489
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 12.47 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.49 (0.39), residues: 417
  helix: -3.34 (0.69), residues: 35
  sheet:  0.06 (0.44), residues: 138
  loop : -1.27 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  50 
 TYR   0.021   0.002   TYR A 365 
 PHE   0.021   0.002   PHE C  98 
 TRP   0.015   0.002   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3388)
  covalent geometry    : angle       0.71273 ( 4605)
  SS BOND              : bond        0.00316 (    6)
  SS BOND              : angle       1.05347 (   12)
  hydrogen bonds       : bond        0.04020 (  107)
  hydrogen bonds       : angle       6.29479 (  252)
  link_NAG-ASN         : bond        0.00203 (    1)
  link_NAG-ASN         : angle       2.23245 (    3)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7152 (ttp-110)
REVERT: A  406 GLU cc_start: 0.8399 (pt0) cc_final: 0.7379 (pt0)
REVERT: A  467 ASP cc_start: 0.7500 (t0) cc_final: 0.6416 (p0)
REVERT: A  468 ILE cc_start: 0.9134 (pt) cc_final: 0.8903 (pt)
REVERT: A  484 GLU cc_start: 0.8082 (pm20) cc_final: 0.7852 (pm20)
REVERT: A  493 GLN cc_start: 0.8703 (tt0) cc_final: 0.8398 (tt0)
REVERT: B   36 TRP cc_start: 0.8979 (m100) cc_final: 0.8030 (m-10)
REVERT: B   48 MET cc_start: 0.8143 (mtp) cc_final: 0.7513 (mtm)
REVERT: B   96 MET cc_start: 0.8086 (mtp) cc_final: 0.7744 (mmm)
REVERT: B  105 GLN cc_start: 0.8723 (tt0) cc_final: 0.8142 (pt0)
  outliers start: 12
  outliers final: 9
  residues processed: 107
  average time/residue: 0.0799
  time to fit residues: 10.1315
Evaluate side-chains
  98 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0040
   chunk 30 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.5992

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.116907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.104690 restraints weight = 8711.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.107640 restraints weight = 4445.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.109532 restraints weight = 2710.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.110825 restraints weight = 1868.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.111693 restraints weight = 1407.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3395  Z= 0.137
  Angle     :  0.629   6.031   4620  Z= 0.335
  Chirality :  0.045   0.160    499
  Planarity :  0.005   0.044    594
  Dihedral  :  6.767  55.368    489
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 15.24 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.11 (0.41), residues: 417
  helix: -2.82 (0.73), residues: 41
  sheet:  0.14 (0.42), residues: 149
  loop : -0.90 (0.41), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 466 
 TYR   0.011   0.001   TYR B 100C
 PHE   0.007   0.001   PHE C  62 
 TRP   0.011   0.002   TRP A 436 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3388)
  covalent geometry    : angle       0.62642 ( 4605)
  SS BOND              : bond        0.00255 (    6)
  SS BOND              : angle       0.86714 (   12)
  hydrogen bonds       : bond        0.03543 (  107)
  hydrogen bonds       : angle       6.04778 (  252)
  link_NAG-ASN         : bond        0.00093 (    1)
  link_NAG-ASN         : angle       1.82832 (    3)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7678 (m110) cc_final: 0.7258 (m110)
REVERT: A  467 ASP cc_start: 0.7329 (t0) cc_final: 0.6378 (p0)
REVERT: A  493 GLN cc_start: 0.8805 (tt0) cc_final: 0.8432 (tt0)
REVERT: B   36 TRP cc_start: 0.8987 (m100) cc_final: 0.8116 (m-10)
REVERT: B   48 MET cc_start: 0.8089 (mtp) cc_final: 0.7379 (mtm)
REVERT: B   61 GLN cc_start: 0.8881 (pm20) cc_final: 0.8369 (pp30)
REVERT: B   99 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8523 (tmm-80)
REVERT: B  105 GLN cc_start: 0.8662 (tt0) cc_final: 0.8237 (pt0)
REVERT: C   89 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7385 (tm-30)
  outliers start: 14
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0787
  time to fit residues: 9.5887
Evaluate side-chains
  98 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue   99 ARG
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0050
   chunk 28 optimal weight:    0.0030
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.5606

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

Flipped N/Q/H residues before XYZ refinement:
** C  55 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 = 0.3700 r_free = 0.3700 target = 0.117219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.105151 restraints weight = 8646.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.107991 restraints weight = 4469.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.109842 restraints weight = 2762.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.111091 restraints weight = 1929.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.111913 restraints weight = 1459.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3395  Z= 0.131
  Angle     :  0.617   6.379   4620  Z= 0.328
  Chirality :  0.044   0.163    499
  Planarity :  0.005   0.045    594
  Dihedral  :  6.496  55.319    489
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 16.07 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.93 (0.42), residues: 417
  helix: -2.67 (0.75), residues: 41
  sheet:  0.18 (0.41), residues: 152
  loop : -0.71 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  50 
 TYR   0.012   0.001   TYR A 451 
 PHE   0.007   0.001   PHE B  29 
 TRP   0.010   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3388)
  covalent geometry    : angle       0.61516 ( 4605)
  SS BOND              : bond        0.00300 (    6)
  SS BOND              : angle       0.86898 (   12)
  hydrogen bonds       : bond        0.03386 (  107)
  hydrogen bonds       : angle       5.96510 (  252)
  link_NAG-ASN         : bond        0.00090 (    1)
  link_NAG-ASN         : angle       1.70106 (    3)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7720 (m110) cc_final: 0.7287 (m110)
REVERT: A  467 ASP cc_start: 0.6994 (t0) cc_final: 0.6360 (p0)
REVERT: A  493 GLN cc_start: 0.8841 (tt0) cc_final: 0.8346 (tt0)
REVERT: B   36 TRP cc_start: 0.8945 (m100) cc_final: 0.8398 (m-10)
REVERT: B  100 ASP cc_start: 0.8432 (p0) cc_final: 0.8065 (p0)
REVERT: B  105 GLN cc_start: 0.8695 (tt0) cc_final: 0.8199 (pt0)
REVERT: C   31 ASN cc_start: 0.7757 (m-40) cc_final: 0.7228 (t0)
  outliers start: 16
  outliers final: 13
  residues processed: 100
  average time/residue: 0.0695
  time to fit residues: 8.3592
Evaluate side-chains
  88 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    0.1980
   chunk 27 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.117377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.105263 restraints weight = 8684.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.108076 restraints weight = 4487.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.109906 restraints weight = 2772.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.111154 restraints weight = 1940.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.112021 restraints weight = 1472.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3395  Z= 0.131
  Angle     :  0.603   5.857   4620  Z= 0.319
  Chirality :  0.044   0.182    499
  Planarity :  0.005   0.047    594
  Dihedral  :  6.343  55.235    489
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 16.34 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.97 (0.41), residues: 417
  helix: -2.69 (0.74), residues: 41
  sheet:  0.09 (0.41), residues: 152
  loop : -0.70 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 403 
 TYR   0.012   0.001   TYR A 451 
 PHE   0.009   0.001   PHE C  62 
 TRP   0.011   0.002   TRP B  47 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3388)
  covalent geometry    : angle       0.60074 ( 4605)
  SS BOND              : bond        0.00315 (    6)
  SS BOND              : angle       0.83112 (   12)
  hydrogen bonds       : bond        0.03348 (  107)
  hydrogen bonds       : angle       5.89201 (  252)
  link_NAG-ASN         : bond        0.00090 (    1)
  link_NAG-ASN         : angle       1.64334 (    3)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7737 (m110) cc_final: 0.7263 (m110)
REVERT: A  403 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7399 (ttp-110)
REVERT: A  423 TYR cc_start: 0.7650 (t80) cc_final: 0.6748 (t80)
REVERT: A  467 ASP cc_start: 0.7119 (t0) cc_final: 0.6372 (p0)
REVERT: A  493 GLN cc_start: 0.8798 (tt0) cc_final: 0.8457 (tt0)
REVERT: B   36 TRP cc_start: 0.8965 (m100) cc_final: 0.8634 (m100)
REVERT: B   82 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6984 (pp)
REVERT: B  105 GLN cc_start: 0.8674 (tt0) cc_final: 0.8154 (pt0)
REVERT: C   31 ASN cc_start: 0.7651 (m-40) cc_final: 0.7045 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 100
  average time/residue: 0.0637
  time to fit residues: 7.6544
Evaluate side-chains
  94 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.115454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.103453 restraints weight = 8710.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.106309 restraints weight = 4472.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.108155 restraints weight = 2738.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.109366 restraints weight = 1898.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.110211 restraints weight = 1438.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3395  Z= 0.166
  Angle     :  0.635   5.999   4620  Z= 0.339
  Chirality :  0.045   0.181    499
  Planarity :  0.005   0.049    594
  Dihedral  :  6.441  55.687    489
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 17.17 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.05 (0.41), residues: 417
  helix: -2.73 (0.74), residues: 41
  sheet:  0.10 (0.41), residues: 155
  loop : -0.81 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 403 
 TYR   0.012   0.001   TYR A 451 
 PHE   0.008   0.001   PHE B  54 
 TRP   0.010   0.002   TRP B  47 
 HIS   0.004   0.003   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 3388)
  covalent geometry    : angle       0.63138 ( 4605)
  SS BOND              : bond        0.00299 (    6)
  SS BOND              : angle       1.16268 (   12)
  hydrogen bonds       : bond        0.03457 (  107)
  hydrogen bonds       : angle       6.09981 (  252)
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       1.80822 (    3)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7757 (m110) cc_final: 0.7282 (m110)
REVERT: A  423 TYR cc_start: 0.7660 (t80) cc_final: 0.6982 (t80)
REVERT: A  467 ASP cc_start: 0.7186 (t70) cc_final: 0.6468 (p0)
REVERT: A  493 GLN cc_start: 0.8879 (tt0) cc_final: 0.8597 (tt0)
REVERT: B   36 TRP cc_start: 0.9065 (m100) cc_final: 0.8620 (m-10)
REVERT: B   48 MET cc_start: 0.8257 (mtp) cc_final: 0.8005 (mtp)
REVERT: B   82 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7073 (pp)
REVERT: B   96 MET cc_start: 0.8462 (mmm) cc_final: 0.8217 (mmm)
REVERT: B  105 GLN cc_start: 0.8660 (tt0) cc_final: 0.8180 (pt0)
REVERT: C   89 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7687 (tm-30)
  outliers start: 22
  outliers final: 20
  residues processed: 99
  average time/residue: 0.0546
  time to fit residues: 6.9289
Evaluate side-chains
  104 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 24 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   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 = 0.3695 r_free = 0.3695 target = 0.117047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.104807 restraints weight = 8854.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.107676 restraints weight = 4553.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.109551 restraints weight = 2786.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.110803 restraints weight = 1927.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.111608 restraints weight = 1458.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3395  Z= 0.136
  Angle     :  0.603   6.337   4620  Z= 0.324
  Chirality :  0.044   0.174    499
  Planarity :  0.005   0.050    594
  Dihedral  :  6.242  54.935    489
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 18.01 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.02 (0.41), residues: 417
  helix: -2.87 (0.65), residues: 47
  sheet:  0.16 (0.42), residues: 146
  loop : -0.68 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 403 
 TYR   0.010   0.001   TYR A 451 
 PHE   0.008   0.001   PHE C  62 
 TRP   0.011   0.001   TRP B  47 
 HIS   0.003   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3388)
  covalent geometry    : angle       0.59942 ( 4605)
  SS BOND              : bond        0.00288 (    6)
  SS BOND              : angle       1.09818 (   12)
  hydrogen bonds       : bond        0.03248 (  107)
  hydrogen bonds       : angle       6.06330 (  252)
  link_NAG-ASN         : bond        0.00092 (    1)
  link_NAG-ASN         : angle       1.63674 (    3)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7787 (m110) cc_final: 0.7307 (m110)
REVERT: A  403 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7411 (ttp-110)
REVERT: A  423 TYR cc_start: 0.7623 (t80) cc_final: 0.7166 (t80)
REVERT: A  467 ASP cc_start: 0.7189 (t70) cc_final: 0.6352 (p0)
REVERT: A  493 GLN cc_start: 0.8902 (tt0) cc_final: 0.8680 (tt0)
REVERT: B   36 TRP cc_start: 0.9032 (m100) cc_final: 0.8658 (m-10)
REVERT: B   82 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7093 (pp)
REVERT: B   96 MET cc_start: 0.8518 (mmm) cc_final: 0.8210 (mmm)
REVERT: B  105 GLN cc_start: 0.8708 (tt0) cc_final: 0.8203 (pt0)
REVERT: C   31 ASN cc_start: 0.7650 (m-40) cc_final: 0.7047 (t0)
REVERT: C   89 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7638 (tm-30)
  outliers start: 20
  outliers final: 19
  residues processed: 98
  average time/residue: 0.0549
  time to fit residues: 6.8549
Evaluate side-chains
  104 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0870
   chunk 15 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0980
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 12 optimal weight:    0.1980
   chunk 26 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.3558

-------------------------------------------------------------------------------
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 = 0.3737 r_free = 0.3737 target = 0.119994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.107938 restraints weight = 8808.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.110785 restraints weight = 4539.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.112648 restraints weight = 2794.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.113957 restraints weight = 1939.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.114815 restraints weight = 1461.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.4642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3395  Z= 0.115
  Angle     :  0.598   6.340   4620  Z= 0.322
  Chirality :  0.044   0.185    499
  Planarity :  0.005   0.051    594
  Dihedral  :  6.003  54.391    489
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 19.67 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.96 (0.41), residues: 417
  helix: -3.13 (0.65), residues: 41
  sheet:  0.24 (0.43), residues: 144
  loop : -0.69 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 403 
 TYR   0.009   0.001   TYR B 100C
 PHE   0.011   0.001   PHE B  29 
 TRP   0.013   0.001   TRP B  47 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3388)
  covalent geometry    : angle       0.59534 ( 4605)
  SS BOND              : bond        0.00214 (    6)
  SS BOND              : angle       1.09964 (   12)
  hydrogen bonds       : bond        0.03179 (  107)
  hydrogen bonds       : angle       6.04698 (  252)
  link_NAG-ASN         : bond        0.00130 (    1)
  link_NAG-ASN         : angle       1.46178 (    3)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7587 (m110) cc_final: 0.7184 (m110)
REVERT: A  403 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7406 (ttp-110)
REVERT: A  406 GLU cc_start: 0.8474 (pt0) cc_final: 0.7869 (pm20)
REVERT: A  423 TYR cc_start: 0.7541 (t80) cc_final: 0.7185 (t80)
REVERT: A  467 ASP cc_start: 0.7146 (t70) cc_final: 0.6389 (p0)
REVERT: A  493 GLN cc_start: 0.8934 (tt0) cc_final: 0.8701 (tt0)
REVERT: B   36 TRP cc_start: 0.8967 (m100) cc_final: 0.8657 (m-10)
REVERT: B   82 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7004 (pp)
REVERT: B  105 GLN cc_start: 0.8628 (tt0) cc_final: 0.8145 (pt0)
REVERT: C   31 ASN cc_start: 0.7461 (m-40) cc_final: 0.6997 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 99
  average time/residue: 0.0612
  time to fit residues: 7.5358
Evaluate side-chains
  102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.114989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.102753 restraints weight = 8830.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.105617 restraints weight = 4589.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.107478 restraints weight = 2830.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.108736 restraints weight = 1963.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.109578 restraints weight = 1482.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.4566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3395  Z= 0.202
  Angle     :  0.680  10.881   4620  Z= 0.365
  Chirality :  0.048   0.317    499
  Planarity :  0.005   0.050    594
  Dihedral  :  6.440  56.179    489
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 19.11 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.17 (0.41), residues: 417
  helix: -2.93 (0.64), residues: 47
  sheet:  0.15 (0.42), residues: 147
  loop : -0.88 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  94 
 TYR   0.012   0.002   TYR A 451 
 PHE   0.010   0.002   PHE A 464 
 TRP   0.013   0.002   TRP A 353 
 HIS   0.006   0.004   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 3388)
  covalent geometry    : angle       0.67481 ( 4605)
  SS BOND              : bond        0.00304 (    6)
  SS BOND              : angle       1.49426 (   12)
  hydrogen bonds       : bond        0.03691 (  107)
  hydrogen bonds       : angle       6.03946 (  252)
  link_NAG-ASN         : bond        0.00075 (    1)
  link_NAG-ASN         : angle       1.92504 (    3)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7804 (m110) cc_final: 0.7392 (m110)
REVERT: A  423 TYR cc_start: 0.7614 (t80) cc_final: 0.7115 (t80)
REVERT: A  467 ASP cc_start: 0.7295 (t70) cc_final: 0.6498 (p0)
REVERT: A  493 GLN cc_start: 0.8886 (tt0) cc_final: 0.8530 (tt0)
REVERT: B   36 TRP cc_start: 0.9125 (m100) cc_final: 0.8664 (m-10)
REVERT: B   82 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7125 (pp)
REVERT: B  105 GLN cc_start: 0.8717 (tt0) cc_final: 0.8223 (pt0)
REVERT: C   31 ASN cc_start: 0.7706 (m-40) cc_final: 0.7069 (t0)
  outliers start: 18
  outliers final: 17
  residues processed: 94
  average time/residue: 0.0602
  time to fit residues: 7.0907
Evaluate side-chains
  99 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    6 GLN
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0170
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5818

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.117704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.105687 restraints weight = 8661.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.108553 restraints weight = 4405.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.110389 restraints weight = 2674.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.111553 restraints weight = 1841.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.112438 restraints weight = 1407.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.4729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3395  Z= 0.140
  Angle     :  0.646   8.167   4620  Z= 0.346
  Chirality :  0.046   0.216    499
  Planarity :  0.005   0.052    594
  Dihedral  :  6.209  54.982    489
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 20.22 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.11 (0.41), residues: 417
  helix: -2.83 (0.66), residues: 47
  sheet:  0.17 (0.41), residues: 154
  loop : -0.86 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 403 
 TYR   0.013   0.001   TYR B 100C
 PHE   0.008   0.001   PHE C  62 
 TRP   0.015   0.002   TRP B  47 
 HIS   0.003   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3388)
  covalent geometry    : angle       0.64245 ( 4605)
  SS BOND              : bond        0.00210 (    6)
  SS BOND              : angle       1.30558 (   12)
  hydrogen bonds       : bond        0.03364 (  107)
  hydrogen bonds       : angle       5.90772 (  252)
  link_NAG-ASN         : bond        0.00065 (    1)
  link_NAG-ASN         : angle       1.59750 (    3)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7682 (m110) cc_final: 0.7314 (m110)
REVERT: A  420 ASP cc_start: 0.7604 (m-30) cc_final: 0.6981 (m-30)
REVERT: A  423 TYR cc_start: 0.7591 (t80) cc_final: 0.7225 (t80)
REVERT: A  467 ASP cc_start: 0.7271 (t70) cc_final: 0.6546 (p0)
REVERT: A  493 GLN cc_start: 0.8832 (tt0) cc_final: 0.8487 (tt0)
REVERT: B   36 TRP cc_start: 0.9082 (m100) cc_final: 0.8630 (m-10)
REVERT: B   82 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7120 (pp)
REVERT: B  105 GLN cc_start: 0.8722 (tt0) cc_final: 0.8235 (pt0)
REVERT: C   31 ASN cc_start: 0.7559 (m-40) cc_final: 0.7011 (t0)
  outliers start: 15
  outliers final: 14
  residues processed: 97
  average time/residue: 0.0582
  time to fit residues: 7.0077
Evaluate side-chains
  101 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0970
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.118049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.105757 restraints weight = 8840.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.108647 restraints weight = 4555.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.110503 restraints weight = 2789.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.111745 restraints weight = 1926.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.112572 restraints weight = 1456.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3395  Z= 0.143
  Angle     :  0.650   7.209   4620  Z= 0.349
  Chirality :  0.045   0.195    499
  Planarity :  0.005   0.052    594
  Dihedral  :  6.167  54.961    489
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 20.50 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.11 (0.41), residues: 417
  helix: -2.78 (0.67), residues: 47
  sheet:  0.24 (0.41), residues: 154
  loop : -0.93 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 403 
 TYR   0.023   0.001   TYR B  32 
 PHE   0.011   0.001   PHE B  29 
 TRP   0.013   0.001   TRP B  47 
 HIS   0.003   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3388)
  covalent geometry    : angle       0.64691 ( 4605)
  SS BOND              : bond        0.00222 (    6)
  SS BOND              : angle       1.25548 (   12)
  hydrogen bonds       : bond        0.03349 (  107)
  hydrogen bonds       : angle       5.92289 (  252)
  link_NAG-ASN         : bond        0.00065 (    1)
  link_NAG-ASN         : angle       1.55236 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 864.62 seconds
wall clock time: 15 minutes 31.55 seconds (931.55 seconds total)