Starting phenix.real_space_refine
on Fri Oct 10 12:10:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7the_25893/10_2025/7the_25893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7the_25893/10_2025/7the_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_25893/10_2025/7the_25893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7the_25893/10_2025/7the_25893.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7the_25893/10_2025/7the_25893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7the_25893/10_2025/7the_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-2.0-5842/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: 1.08, per 1000 atoms: 0.33
  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: 0.25
  Conformation dependent library (CDL) restraints added in 133.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.19
  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: 0.42

  Time building geometry restraints manager: 0.36 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:             2.630
  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:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.320
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.360
-------------------------------------------------------------------------------
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 aren 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  : 0.126 
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: 0.7517 (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: 0.0919
  time to fit residues: 13.5887
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 aren 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  : 0.112 
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: 0.8702 (tt0) cc_final: 0.8398 (tt0)
REVERT: B   12 LYS cc_start: 0.6992 (mttm) cc_final: 0.6792 (mttm)
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: 0.7743 (mmm)
REVERT: B  105 GLN cc_start: 0.8722 (tt0) cc_final: 0.8142 (pt0)
  outliers start: 12
  outliers final: 9
  residues processed: 107
  average time/residue: 0.0799
  time to fit residues: 10.0236
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  : 0.080 
-------------------------------------------------------------------------------
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...

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 = 0.3697 r_free = 0.3697 target = 0.117212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.104971 restraints weight = 8709.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.107909 restraints weight = 4460.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.109820 restraints weight = 2726.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.111120 restraints weight = 1875.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.111981 restraints weight = 1416.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3445

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= 0.136
  Angle     :  0.625   6.039   4620  Z= 0.334
  Chirality :  0.045   0.159    499
  Planarity :  0.005   0.044    594
  Dihedral  :  6.727  55.314    489
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  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 aren not related in a simple way.
  whole: -1.08 (0.41), residues: 417
  helix: -2.80 (0.73), residues: 41
  sheet:  0.16 (0.41), residues: 154
  loop : -0.89 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  50 
 TYR   0.011   0.001   TYR A 423 
 PHE   0.008   0.001   PHE C  62 
 TRP   0.011   0.002   TRP B  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3388)
  covalent geometry    : angle       0.62281 ( 4605)
  SS BOND              : bond        0.00288 (    6)
  SS BOND              : angle       0.83858 (   12)
  hydrogen bonds       : bond        0.03525 (  107)
  hydrogen bonds       : angle       6.03353 (  252)
  link_NAG-ASN         : bond        0.00091 (    1)
  link_NAG-ASN         : angle       1.80557 (    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  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7675 (m110) cc_final: 0.7237 (m110)
REVERT: A  467 ASP cc_start: 0.7315 (t0) cc_final: 0.6393 (p0)
REVERT: A  493 GLN cc_start: 0.8809 (tt0) cc_final: 0.8429 (tt0)
REVERT: B   36 TRP cc_start: 0.8987 (m100) cc_final: 0.8151 (m-10)
REVERT: B   48 MET cc_start: 0.8079 (mtp) cc_final: 0.7376 (mtm)
REVERT: B   61 GLN cc_start: 0.8869 (pm20) cc_final: 0.8348 (pp30)
REVERT: B   96 MET cc_start: 0.8220 (mtp) cc_final: 0.7951 (mmm)
REVERT: B  105 GLN cc_start: 0.8658 (tt0) cc_final: 0.8237 (pt0)
REVERT: C   89 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7399 (tm-30)
  outliers start: 14
  outliers final: 12
  residues processed: 103
  average time/residue: 0.0826
  time to fit residues: 10.1333
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  : 0.137 
-------------------------------------------------------------------------------
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 12 optimal weight:    0.3980
   chunk 35 optimal weight:    0.6980
   chunk 2 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3691 r_free = 0.3691 target = 0.116586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.104520 restraints weight = 8588.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.107330 restraints weight = 4432.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.109198 restraints weight = 2739.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.110452 restraints weight = 1902.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.111305 restraints weight = 1433.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3395  Z= 0.144
  Angle     :  0.624   6.323   4620  Z= 0.332
  Chirality :  0.044   0.162    499
  Planarity :  0.005   0.047    594
  Dihedral  :  6.560  55.562    489
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 16.34 %
    Favored  : 78.95 %
  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 aren not related in a simple way.
  whole: -0.89 (0.42), residues: 417
  helix: -2.64 (0.76), residues: 41
  sheet:  0.20 (0.41), residues: 151
  loop : -0.69 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  50 
 TYR   0.016   0.002   TYR A 451 
 PHE   0.008   0.001   PHE B  29 
 TRP   0.010   0.002   TRP A 436 
 HIS   0.002   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3388)
  covalent geometry    : angle       0.62172 ( 4605)
  SS BOND              : bond        0.00338 (    6)
  SS BOND              : angle       0.87512 (   12)
  hydrogen bonds       : bond        0.03427 (  107)
  hydrogen bonds       : angle       6.00901 (  252)
  link_NAG-ASN         : bond        0.00071 (    1)
  link_NAG-ASN         : angle       1.75556 (    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
  109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7713 (m110) cc_final: 0.7287 (m110)
REVERT: A  467 ASP cc_start: 0.7106 (t0) cc_final: 0.6387 (p0)
REVERT: A  493 GLN cc_start: 0.8817 (tt0) cc_final: 0.8282 (tt0)
REVERT: B   36 TRP cc_start: 0.8989 (m100) cc_final: 0.8432 (m-10)
REVERT: B   99 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8556 (tmm-80)
REVERT: B  105 GLN cc_start: 0.8698 (tt0) cc_final: 0.8192 (pt0)
  outliers start: 17
  outliers final: 14
  residues processed: 101
  average time/residue: 0.0722
  time to fit residues: 8.7211
Evaluate side-chains
  93 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
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   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
Chi-restraints excluded: chain C residue  104 LEU
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:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.115859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.103742 restraints weight = 8734.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.106563 restraints weight = 4497.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.108388 restraints weight = 2786.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.109633 restraints weight = 1948.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.110443 restraints weight = 1480.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3395  Z= 0.156
  Angle     :  0.620   5.949   4620  Z= 0.330
  Chirality :  0.044   0.182    499
  Planarity :  0.005   0.048    594
  Dihedral  :  6.509  55.629    489
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 16.62 %
    Favored  : 77.29 %
  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 aren not related in a simple way.
  whole: -1.08 (0.41), residues: 417
  helix: -2.67 (0.75), residues: 41
  sheet:  0.02 (0.42), residues: 152
  loop : -0.79 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 403 
 TYR   0.012   0.001   TYR A 451 
 PHE   0.008   0.001   PHE C  62 
 TRP   0.011   0.002   TRP B  47 
 HIS   0.004   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3388)
  covalent geometry    : angle       0.61780 ( 4605)
  SS BOND              : bond        0.00273 (    6)
  SS BOND              : angle       0.89686 (   12)
  hydrogen bonds       : bond        0.03501 (  107)
  hydrogen bonds       : angle       5.98795 (  252)
  link_NAG-ASN         : bond        0.00046 (    1)
  link_NAG-ASN         : angle       1.78588 (    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
  109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7762 (m110) cc_final: 0.7336 (m110)
REVERT: A  423 TYR cc_start: 0.7687 (t80) cc_final: 0.6796 (t80)
REVERT: A  467 ASP cc_start: 0.7242 (t70) cc_final: 0.6451 (p0)
REVERT: A  493 GLN cc_start: 0.8781 (tt0) cc_final: 0.8365 (tt0)
REVERT: B   36 TRP cc_start: 0.9041 (m100) cc_final: 0.8661 (m-10)
REVERT: B   82 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7142 (pp)
REVERT: B   99 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8869 (tmm-80)
REVERT: B  100 ASP cc_start: 0.8536 (p0) cc_final: 0.8197 (p0)
REVERT: B  105 GLN cc_start: 0.8675 (tt0) cc_final: 0.8215 (pt0)
  outliers start: 22
  outliers final: 17
  residues processed: 102
  average time/residue: 0.0770
  time to fit residues: 9.4075
Evaluate side-chains
  99 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
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 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   80 LEU
Chi-restraints excluded: chain B residue   82 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
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:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   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 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.116067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.104122 restraints weight = 8621.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.106936 restraints weight = 4398.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.108759 restraints weight = 2700.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.110008 restraints weight = 1879.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.110891 restraints weight = 1418.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.4289

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= 0.144
  Angle     :  0.602   5.729   4620  Z= 0.322
  Chirality :  0.044   0.176    499
  Planarity :  0.005   0.048    594
  Dihedral  :  6.357  55.388    489
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 17.45 %
    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 aren not related in a simple way.
  whole: -1.09 (0.41), residues: 417
  helix: -3.10 (0.71), residues: 35
  sheet:  0.03 (0.42), residues: 150
  loop : -0.80 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 403 
 TYR   0.010   0.001   TYR A 451 
 PHE   0.008   0.001   PHE C  62 
 TRP   0.011   0.002   TRP B  47 
 HIS   0.004   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3388)
  covalent geometry    : angle       0.59987 ( 4605)
  SS BOND              : bond        0.00286 (    6)
  SS BOND              : angle       0.84045 (   12)
  hydrogen bonds       : bond        0.03353 (  107)
  hydrogen bonds       : angle       5.97414 (  252)
  link_NAG-ASN         : bond        0.00049 (    1)
  link_NAG-ASN         : angle       1.73409 (    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
  108 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7819 (m110) cc_final: 0.7363 (m110)
REVERT: A  423 TYR cc_start: 0.7676 (t80) cc_final: 0.6958 (t80)
REVERT: A  467 ASP cc_start: 0.7193 (t70) cc_final: 0.6290 (p0)
REVERT: A  493 GLN cc_start: 0.8804 (tt0) cc_final: 0.8476 (tt0)
REVERT: B   36 TRP cc_start: 0.9044 (m100) cc_final: 0.8649 (m-10)
REVERT: B   48 MET cc_start: 0.8278 (mtp) cc_final: 0.8070 (mtp)
REVERT: B   82 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7148 (pp)
REVERT: B   99 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8833 (tmm-80)
REVERT: B  100 ASP cc_start: 0.8390 (p0) cc_final: 0.8072 (p0)
REVERT: B  105 GLN cc_start: 0.8650 (tt0) cc_final: 0.8206 (pt0)
  outliers start: 21
  outliers final: 17
  residues processed: 100
  average time/residue: 0.0596
  time to fit residues: 7.4647
Evaluate side-chains
  100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
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  478 THR
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   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   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
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:    0.9980
   chunk 35 optimal weight:    0.0980
   chunk 8 optimal weight:    0.4980
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.117181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.104996 restraints weight = 8783.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.107864 restraints weight = 4510.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.109760 restraints weight = 2759.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.111022 restraints weight = 1908.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.111686 restraints weight = 1440.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3395  Z= 0.127
  Angle     :  0.587   6.403   4620  Z= 0.314
  Chirality :  0.043   0.153    499
  Planarity :  0.005   0.051    594
  Dihedral  :  6.204  54.899    489
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 18.56 %
    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 aren not related in a simple way.
  whole: -1.11 (0.41), residues: 417
  helix: -3.15 (0.69), residues: 35
  sheet:  0.00 (0.42), residues: 150
  loop : -0.80 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 403 
 TYR   0.009   0.001   TYR B  95 
 PHE   0.008   0.001   PHE C  62 
 TRP   0.013   0.002   TRP B  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3388)
  covalent geometry    : angle       0.58334 ( 4605)
  SS BOND              : bond        0.00225 (    6)
  SS BOND              : angle       1.21184 (   12)
  hydrogen bonds       : bond        0.03244 (  107)
  hydrogen bonds       : angle       5.92931 (  252)
  link_NAG-ASN         : bond        0.00106 (    1)
  link_NAG-ASN         : angle       1.57592 (    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
  110 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7706 (m110) cc_final: 0.7276 (m110)
REVERT: A  423 TYR cc_start: 0.7616 (t80) cc_final: 0.7088 (t80)
REVERT: A  467 ASP cc_start: 0.7046 (t70) cc_final: 0.6341 (p0)
REVERT: A  493 GLN cc_start: 0.8830 (tt0) cc_final: 0.8521 (tt0)
REVERT: B   36 TRP cc_start: 0.9024 (m100) cc_final: 0.8636 (m-10)
REVERT: B   82 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7185 (pp)
REVERT: B   99 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8815 (tmm-80)
REVERT: B  100 ASP cc_start: 0.8198 (p0) cc_final: 0.7840 (p0)
REVERT: B  105 GLN cc_start: 0.8702 (tt0) cc_final: 0.8204 (pt0)
REVERT: C   31 ASN cc_start: 0.7611 (m-40) cc_final: 0.7061 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 102
  average time/residue: 0.0648
  time to fit residues: 8.2145
Evaluate side-chains
  100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  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  382 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   80 LEU
Chi-restraints excluded: chain B residue   82 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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 36 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0000
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.6186

-------------------------------------------------------------------------------
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 = 0.117173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.105059 restraints weight = 8845.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.107849 restraints weight = 4550.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.109711 restraints weight = 2799.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.110949 restraints weight = 1947.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.111820 restraints weight = 1480.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.4563

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= 0.134
  Angle     :  0.595   6.078   4620  Z= 0.321
  Chirality :  0.044   0.151    499
  Planarity :  0.005   0.051    594
  Dihedral  :  6.208  55.000    489
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 18.84 %
    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 aren not related in a simple way.
  whole: -1.10 (0.41), residues: 417
  helix: -3.22 (0.68), residues: 35
  sheet:  0.12 (0.43), residues: 144
  loop : -0.83 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 403 
 TYR   0.008   0.001   TYR B  95 
 PHE   0.010   0.001   PHE B  29 
 TRP   0.014   0.002   TRP B  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3388)
  covalent geometry    : angle       0.59133 ( 4605)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       1.18572 (   12)
  hydrogen bonds       : bond        0.03353 (  107)
  hydrogen bonds       : angle       5.95098 (  252)
  link_NAG-ASN         : bond        0.00077 (    1)
  link_NAG-ASN         : angle       1.60808 (    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
  106 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7689 (m110) cc_final: 0.7264 (m110)
REVERT: A  423 TYR cc_start: 0.7608 (t80) cc_final: 0.7162 (t80)
REVERT: A  467 ASP cc_start: 0.7098 (t70) cc_final: 0.6373 (p0)
REVERT: A  493 GLN cc_start: 0.8837 (tt0) cc_final: 0.8426 (tt0)
REVERT: B   36 TRP cc_start: 0.9041 (m100) cc_final: 0.8620 (m-10)
REVERT: B   99 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8807 (tmm-80)
REVERT: B  100 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8782 (mm-40)
REVERT: B  100 ASP cc_start: 0.8157 (p0) cc_final: 0.7812 (p0)
REVERT: B  105 GLN cc_start: 0.8693 (tt0) cc_final: 0.8224 (pt0)
REVERT: C   31 ASN cc_start: 0.7537 (m-40) cc_final: 0.7019 (t0)
REVERT: C   89 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7768 (tm-30)
  outliers start: 19
  outliers final: 15
  residues processed: 98
  average time/residue: 0.0688
  time to fit residues: 8.2255
Evaluate side-chains
  100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
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  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   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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 38 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0030
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6190

-------------------------------------------------------------------------------
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 = 0.117302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.105185 restraints weight = 8770.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.107997 restraints weight = 4513.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.109843 restraints weight = 2771.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.111060 restraints weight = 1922.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.111929 restraints weight = 1462.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.4653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3395  Z= 0.136
  Angle     :  0.611   6.200   4620  Z= 0.329
  Chirality :  0.044   0.152    499
  Planarity :  0.005   0.052    594
  Dihedral  :  6.204  54.985    489
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 18.56 %
    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 aren not related in a simple way.
  whole: -1.18 (0.41), residues: 417
  helix: -3.26 (0.62), residues: 41
  sheet:  0.14 (0.42), residues: 150
  loop : -0.89 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  94 
 TYR   0.016   0.001   TYR C  92 
 PHE   0.008   0.001   PHE C  62 
 TRP   0.013   0.002   TRP B  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3388)
  covalent geometry    : angle       0.60755 ( 4605)
  SS BOND              : bond        0.00224 (    6)
  SS BOND              : angle       1.23078 (   12)
  hydrogen bonds       : bond        0.03302 (  107)
  hydrogen bonds       : angle       6.04558 (  252)
  link_NAG-ASN         : bond        0.00079 (    1)
  link_NAG-ASN         : angle       1.57847 (    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
  104 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7672 (m110) cc_final: 0.7249 (m110)
REVERT: A  423 TYR cc_start: 0.7585 (t80) cc_final: 0.7171 (t80)
REVERT: A  467 ASP cc_start: 0.7166 (t70) cc_final: 0.6464 (p0)
REVERT: A  493 GLN cc_start: 0.8818 (tt0) cc_final: 0.8390 (tt0)
REVERT: B   36 TRP cc_start: 0.9050 (m100) cc_final: 0.8667 (m-10)
REVERT: B   99 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8825 (tmm-80)
REVERT: B  100 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8765 (mm-40)
REVERT: B  100 ASP cc_start: 0.8158 (p0) cc_final: 0.7824 (p0)
REVERT: B  105 GLN cc_start: 0.8692 (tt0) cc_final: 0.8197 (pt0)
REVERT: C   31 ASN cc_start: 0.7569 (m-40) cc_final: 0.7044 (t0)
REVERT: C   89 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7742 (tm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 97
  average time/residue: 0.0591
  time to fit residues: 7.0443
Evaluate side-chains
  98 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  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  382 VAL
Chi-restraints excluded: chain A residue  393 THR
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   97 VAL
Chi-restraints excluded: chain B residue   99 ARG
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 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.117044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.104848 restraints weight = 8766.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.107676 restraints weight = 4531.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.109519 restraints weight = 2779.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.110742 restraints weight = 1933.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.111589 restraints weight = 1469.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.4766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3395  Z= 0.144
  Angle     :  0.627   8.445   4620  Z= 0.335
  Chirality :  0.044   0.152    499
  Planarity :  0.005   0.052    594
  Dihedral  :  6.258  55.221    489
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 18.84 %
    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 aren not related in a simple way.
  whole: -1.14 (0.41), residues: 417
  helix: -2.90 (0.65), residues: 47
  sheet:  0.22 (0.42), residues: 149
  loop : -0.90 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 403 
 TYR   0.021   0.001   TYR C  92 
 PHE   0.012   0.001   PHE B  29 
 TRP   0.013   0.002   TRP B  47 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3388)
  covalent geometry    : angle       0.62212 ( 4605)
  SS BOND              : bond        0.00240 (    6)
  SS BOND              : angle       1.44001 (   12)
  hydrogen bonds       : bond        0.03375 (  107)
  hydrogen bonds       : angle       6.22003 (  252)
  link_NAG-ASN         : bond        0.00001 (    1)
  link_NAG-ASN         : angle       1.65766 (    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
  105 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7651 (m110) cc_final: 0.7243 (m110)
REVERT: A  423 TYR cc_start: 0.7611 (t80) cc_final: 0.7209 (t80)
REVERT: A  467 ASP cc_start: 0.7196 (t70) cc_final: 0.6455 (p0)
REVERT: A  493 GLN cc_start: 0.8828 (tt0) cc_final: 0.8426 (tt0)
REVERT: B   36 TRP cc_start: 0.9082 (m100) cc_final: 0.8677 (m-10)
REVERT: B   99 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8793 (tmm-80)
REVERT: B  100 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8745 (mm-40)
REVERT: B  100 ASP cc_start: 0.8158 (p0) cc_final: 0.7834 (p0)
REVERT: B  105 GLN cc_start: 0.8765 (tt0) cc_final: 0.8227 (pt0)
REVERT: C   31 ASN cc_start: 0.7528 (m-40) cc_final: 0.7019 (t0)
  outliers start: 17
  outliers final: 15
  residues processed: 98
  average time/residue: 0.0657
  time to fit residues: 7.7400
Evaluate side-chains
  100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
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  402 ILE
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   97 VAL
Chi-restraints excluded: chain B residue   99 ARG
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:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0050
   chunk 23 optimal weight:    0.2980
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.118029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.105885 restraints weight = 8845.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.108713 restraints weight = 4527.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.110559 restraints weight = 2771.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.111813 restraints weight = 1912.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.112681 restraints weight = 1441.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3395  Z= 0.132
  Angle     :  0.613   6.241   4620  Z= 0.330
  Chirality :  0.044   0.153    499
  Planarity :  0.005   0.052    594
  Dihedral  :  6.178  54.675    489
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 18.84 %
    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 aren not related in a simple way.
  whole: -1.11 (0.41), residues: 417
  helix: -2.85 (0.66), residues: 47
  sheet:  0.18 (0.42), residues: 152
  loop : -0.86 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  94 
 TYR   0.025   0.001   TYR C  92 
 PHE   0.009   0.001   PHE A 347 
 TRP   0.013   0.002   TRP B  47 
 HIS   0.004   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3388)
  covalent geometry    : angle       0.60864 ( 4605)
  SS BOND              : bond        0.00226 (    6)
  SS BOND              : angle       1.32988 (   12)
  hydrogen bonds       : bond        0.03297 (  107)
  hydrogen bonds       : angle       5.98287 (  252)
  link_NAG-ASN         : bond        0.00048 (    1)
  link_NAG-ASN         : angle       1.51678 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 869.80 seconds
wall clock time: 15 minutes 38.40 seconds (938.40 seconds total)