Starting phenix.real_space_refine
on Fri Aug 22 13:32:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i3s_35155/08_2025/8i3s_35155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i3s_35155/08_2025/8i3s_35155.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i3s_35155/08_2025/8i3s_35155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i3s_35155/08_2025/8i3s_35155.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i3s_35155/08_2025/8i3s_35155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i3s_35155/08_2025/8i3s_35155.map"
  }
  resolution = 3.9
  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=  -0.003 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2074      2.51       5
     N     554      2.21       5
     O     628      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3272
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1552
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "H"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 897
          Classifications: {'peptide': 118}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 112}
    Chain: "L"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 809
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.87, per 1000 atoms: 0.27
  Number of scatterers: 3272
  At special positions: 0
  Unit cell: (67.45, 68.4, 96.9, 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      16     16.00
     O     628      8.00
     N     554      7.00
     C    2074      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=1.56
    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 H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  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 A1301 " - " ASN A 343 "
  Time building additional restraints: 0.26
  Conformation dependent library (CDL) restraints added in 130.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      10.7% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 344
      removed outlier: 3.873A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 3.658A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 411
      removed outlier: 3.542A  pdb=" N   GLN A 409 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE A 410 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 4.000A  pdb=" N   THR H  87 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.725A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ARG A 509 " --> pdb=" O   TRP A 436 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TRP A 436 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 7.189A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    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 'H' and resid 6 through 7
      removed outlier: 3.679A  pdb=" N   VAL H  18 " --> pdb=" O   LEU H  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 13
      removed outlier: 7.060A  pdb=" N   LYS H  12 " --> pdb=" O   SER H 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 56 through 59
      removed outlier: 3.670A  pdb=" N   ARG H  56 " --> pdb=" O   ILE H  52 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE H  52 " --> pdb=" O   ARG H  56 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   TYR H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   ARG H  38 " --> pdb=" O   TYR H  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 20 through 24
    Processing sheet with id=AA9, first strand: chain 'L' and resid 45 through 46

    82 hydrogen bonds defined for protein.
    207 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: 0.33

  Time building geometry restraints manager: 0.37 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: 863
        1.33 -     1.45: 679
        1.45 -     1.57: 1787
        1.57 -     1.69: 0
        1.69 -     1.82: 20
  Bond restraints: 3349
  Sorted by residual:
  bond pdb=" N   PRO L  59 "
       pdb=" CA  PRO L  59 "
    ideal  model  delta    sigma   weight residual
    1.468  1.440  0.027 7.90e-03 1.60e+04 1.21e+01
  bond pdb=" N   ASN H  32 "
       pdb=" CA  ASN H  32 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.19e-02 7.06e+03 1.02e+01
  bond pdb=" N   PHE L  62 "
       pdb=" CA  PHE L  62 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.21e-02 6.83e+03 6.49e+00
  bond pdb=" N   ILE L  58 "
       pdb=" CA  ILE L  58 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 1.23e-02 6.61e+03 5.41e+00
  bond pdb=" CA  SER L  63 "
       pdb=" CB  SER L  63 "
    ideal  model  delta    sigma   weight residual
    1.529  1.499  0.030 1.54e-02 4.22e+03 3.78e+00
  ... (remaining 3344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 4343
        1.17 -     2.34: 152
        2.34 -     3.51: 38
        3.51 -     4.68: 10
        4.68 -     5.85: 4
  Bond angle restraints: 4547
  Sorted by residual:
  angle pdb=" CA  ALA L  60 "
        pdb=" C   ALA L  60 "
        pdb=" O   ALA L  60 "
      ideal   model   delta    sigma   weight residual
     120.81  116.22    4.59 1.15e+00 7.56e-01 1.60e+01
  angle pdb=" N   PRO L  59 "
        pdb=" CA  PRO L  59 "
        pdb=" C   PRO L  59 "
      ideal   model   delta    sigma   weight residual
     113.12  107.27    5.85 1.65e+00 3.67e-01 1.26e+01
  angle pdb=" CA  PRO L  59 "
        pdb=" C   PRO L  59 "
        pdb=" O   PRO L  59 "
      ideal   model   delta    sigma   weight residual
     121.38  118.69    2.69 7.70e-01 1.69e+00 1.22e+01
  angle pdb=" C   ILE H  31 "
        pdb=" N   ASN H  32 "
        pdb=" CA  ASN H  32 "
      ideal   model   delta    sigma   weight residual
     122.87  117.62    5.25 1.61e+00 3.86e-01 1.06e+01
  angle pdb=" N   PRO L  59 "
        pdb=" CD  PRO L  59 "
        pdb=" CG  PRO L  59 "
      ideal   model   delta    sigma   weight residual
     103.20   98.41    4.79 1.50e+00 4.44e-01 1.02e+01
  ... (remaining 4542 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.35: 1779
       12.35 -    24.70: 150
       24.70 -    37.05: 50
       37.05 -    49.40: 12
       49.40 -    61.75: 9
  Dihedral angle restraints: 2000
    sinusoidal: 789
      harmonic: 1211
  Sorted by residual:
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -114.61   28.61     1      1.00e+01 1.00e-02 1.17e+01
  dihedral pdb=" CA  ARG L  61 "
           pdb=" CB  ARG L  61 "
           pdb=" CG  ARG L  61 "
           pdb=" CD  ARG L  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  123.29   56.71     3      1.50e+01 4.44e-03 9.41e+00
  dihedral pdb=" CA  ILE A 434 "
           pdb=" CB  ILE A 434 "
           pdb=" CG1 ILE A 434 "
           pdb=" CD1 ILE A 434 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  115.51  -55.51     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 1997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 387
       0.046 -    0.092: 74
       0.092 -    0.138: 31
       0.138 -    0.184: 4
       0.184 -    0.230: 1
  Chirality restraints: 497
  Sorted by residual:
  chirality pdb=" CA  PHE L  62 "
            pdb=" N   PHE L  62 "
            pdb=" C   PHE L  62 "
            pdb=" CB  PHE L  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  ALA L  60 "
            pdb=" N   ALA L  60 "
            pdb=" C   ALA L  60 "
            pdb=" CB  ALA L  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.67   -0.18 2.00e-01 2.50e+01 8.11e-01
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.51e-01
  ... (remaining 494 not shown)

  Planarity restraints: 590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR L  56 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.88e+00
        pdb=" C   THR L  56 "    0.034 2.00e-02 2.50e+03
        pdb=" O   THR L  56 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY L  57 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE H  31 "    0.010 2.00e-02 2.50e+03   1.92e-02 3.69e+00
        pdb=" C   ILE H  31 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ILE H  31 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASN H  32 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H 101 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO H 102 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO H 102 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO H 102 "    0.023 5.00e-02 4.00e+02
  ... (remaining 587 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 560
        2.77 -     3.30: 3130
        3.30 -     3.83: 5250
        3.83 -     4.37: 6115
        4.37 -     4.90: 10669
  Nonbonded interactions: 25724
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 367 "
            pdb=" OG  SER A 371 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG  SER A 349 "
            pdb=" O   LEU A 452 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" NH2 ARG A 457 "
            pdb=" OD2 ASP A 467 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" O   ASP L  82 "
            pdb=" OH  TYR L  86 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" OH  TYR A 453 "
            pdb=" OE1 GLN A 493 "
     model   vdw
     2.369 3.040
  ... (remaining 25719 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:             3.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.400
  Find NCS groups from input model:        0.010
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
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      :  0.009   0.475   3356  Z= 0.457
  Angle     :  0.984  49.602   4562  Z= 0.514
  Chirality :  0.045   0.230    497
  Planarity :  0.004   0.046    589
  Dihedral  : 11.402  61.753   1214
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.02 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.41), residues: 414
  helix: -2.41 (0.71), residues: 38
  sheet: -0.53 (0.53), residues: 110
  loop : -0.60 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  50 
 TYR   0.010   0.001   TYR L  49 
 PHE   0.009   0.001   PHE A 515 
 TRP   0.018   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3349)
  covalent geometry    : angle       0.58682 ( 4547)
  SS BOND              : bond        0.19373 (    6)
  SS BOND              : angle      15.41414 (   12)
  hydrogen bonds       : bond        0.28302 (   82)
  hydrogen bonds       : angle      12.28426 (  207)
  link_NAG-ASN         : bond        0.00233 (    1)
  link_NAG-ASN         : angle       1.13577 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.8021 (t80) cc_final: 0.7525 (t80)
REVERT: A  368 LEU cc_start: 0.5658 (mm) cc_final: 0.5446 (mm)
REVERT: A  458 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8652 (mmtm)
REVERT: A  507 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8078 (Cg_endo)
REVERT: H   10 GLU cc_start: 0.3299 (tt0) cc_final: 0.3026 (mt-10)
REVERT: H   29 PHE cc_start: 0.7177 (m-80) cc_final: 0.6948 (m-10)
REVERT: H   46 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7206 (mt-10)
REVERT: H   79 TYR cc_start: 0.7709 (m-80) cc_final: 0.6961 (m-80)
REVERT: L    4 MET cc_start: 0.7409 (mmm) cc_final: 0.6974 (tpp)
REVERT: L   18 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.7002 (tpp-160)
REVERT: L   36 TYR cc_start: 0.8654 (m-10) cc_final: 0.8422 (m-10)
REVERT: L   49 TYR cc_start: 0.8499 (p90) cc_final: 0.8086 (p90)
REVERT: L   87 TYR cc_start: 0.8368 (m-80) cc_final: 0.8134 (m-10)
  outliers start: 9
  outliers final: 3
  residues processed: 139
  average time/residue: 0.0818
  time to fit residues: 13.1494
Evaluate side-chains
  105 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain L residue    3 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0970
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  61 GLN
L  79 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.139131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.123183 restraints weight = 7136.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.126450 restraints weight = 4152.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.128823 restraints weight = 2816.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130408 restraints weight = 2078.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.131602 restraints weight = 1644.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3356  Z= 0.145
  Angle     :  0.589   5.071   4562  Z= 0.311
  Chirality :  0.046   0.164    497
  Planarity :  0.006   0.058    589
  Dihedral  :  4.827  39.778    490
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 17.80 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.40), residues: 414
  helix: -1.77 (0.80), residues: 37
  sheet: -0.08 (0.54), residues: 97
  loop : -0.85 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 346 
 TYR   0.014   0.001   TYR A 380 
 PHE   0.016   0.002   PHE A 464 
 TRP   0.009   0.001   TRP H  36 
 HIS   0.001   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3349)
  covalent geometry    : angle       0.58706 ( 4547)
  SS BOND              : bond        0.00512 (    6)
  SS BOND              : angle       1.08353 (   12)
  hydrogen bonds       : bond        0.04505 (   82)
  hydrogen bonds       : angle       8.20578 (  207)
  link_NAG-ASN         : bond        0.00144 (    1)
  link_NAG-ASN         : angle       1.08680 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.7958 (ttt90) cc_final: 0.6996 (ttm170)
REVERT: A  374 PHE cc_start: 0.7099 (m-10) cc_final: 0.6888 (m-10)
REVERT: A  464 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6393 (t80)
REVERT: A  474 GLN cc_start: 0.6314 (mt0) cc_final: 0.5893 (mm-40)
REVERT: A  507 PRO cc_start: 0.8153 (Cg_exo) cc_final: 0.7874 (Cg_endo)
REVERT: A  509 ARG cc_start: 0.8712 (ptp-170) cc_final: 0.8328 (mtp180)
REVERT: H   29 PHE cc_start: 0.7102 (m-80) cc_final: 0.6872 (m-10)
REVERT: H   79 TYR cc_start: 0.7430 (m-80) cc_final: 0.6744 (m-80)
REVERT: L    4 MET cc_start: 0.7497 (mmm) cc_final: 0.7137 (tpp)
REVERT: L   11 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7141 (tm)
REVERT: L   18 ARG cc_start: 0.7781 (ttp-170) cc_final: 0.6995 (tpp-160)
  outliers start: 17
  outliers final: 8
  residues processed: 110
  average time/residue: 0.0682
  time to fit residues: 8.9161
Evaluate side-chains
  105 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0070
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    0.2980
   overall best weight:    0.8002

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN
H   6 GLN
H  61 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  93 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.140034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.123166 restraints weight = 6972.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.126432 restraints weight = 4225.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.128757 restraints weight = 2960.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.130299 restraints weight = 2257.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.131515 restraints weight = 1839.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3356  Z= 0.172
  Angle     :  0.618   6.508   4562  Z= 0.320
  Chirality :  0.046   0.182    497
  Planarity :  0.005   0.048    589
  Dihedral  :  5.006  41.142    488
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 18.93 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.39), residues: 414
  helix: -1.61 (0.95), residues: 31
  sheet: -0.21 (0.53), residues: 94
  loop : -0.90 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 346 
 TYR   0.013   0.002   TYR A 489 
 PHE   0.015   0.001   PHE A 338 
 TRP   0.004   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3349)
  covalent geometry    : angle       0.61677 ( 4547)
  SS BOND              : bond        0.00273 (    6)
  SS BOND              : angle       0.86714 (   12)
  hydrogen bonds       : bond        0.04015 (   82)
  hydrogen bonds       : angle       7.34160 (  207)
  link_NAG-ASN         : bond        0.00106 (    1)
  link_NAG-ASN         : angle       1.29290 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A  464 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.6104 (t80)
REVERT: A  474 GLN cc_start: 0.6271 (mt0) cc_final: 0.5802 (mm-40)
REVERT: H   29 PHE cc_start: 0.7182 (m-80) cc_final: 0.6938 (m-10)
REVERT: H   79 TYR cc_start: 0.7283 (m-80) cc_final: 0.6761 (m-80)
REVERT: H  100 TYR cc_start: 0.7364 (p90) cc_final: 0.7156 (p90)
REVERT: L    4 MET cc_start: 0.7467 (mmm) cc_final: 0.7136 (tpp)
REVERT: L   11 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7222 (tm)
REVERT: L   18 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.6926 (tpp-160)
  outliers start: 23
  outliers final: 11
  residues processed: 110
  average time/residue: 0.0643
  time to fit residues: 8.3795
Evaluate side-chains
  103 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
H  61 GLN
L  79 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.140161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.123302 restraints weight = 7048.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.126639 restraints weight = 4237.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.128973 restraints weight = 2951.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.130589 restraints weight = 2253.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.131358 restraints weight = 1810.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3356  Z= 0.160
  Angle     :  0.593   5.165   4562  Z= 0.306
  Chirality :  0.046   0.187    497
  Planarity :  0.005   0.046    589
  Dihedral  :  4.965  40.669    488
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  7.06 %
    Allowed  : 19.49 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.09 (0.40), residues: 414
  helix: -1.34 (1.12), residues: 25
  sheet: -0.18 (0.52), residues: 94
  loop : -0.87 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 346 
 TYR   0.013   0.001   TYR A 423 
 PHE   0.007   0.001   PHE A 374 
 TRP   0.004   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3349)
  covalent geometry    : angle       0.59161 ( 4547)
  SS BOND              : bond        0.00265 (    6)
  SS BOND              : angle       0.77359 (   12)
  hydrogen bonds       : bond        0.03486 (   82)
  hydrogen bonds       : angle       6.99902 (  207)
  link_NAG-ASN         : bond        0.00137 (    1)
  link_NAG-ASN         : angle       1.29667 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.6010 (t80)
REVERT: H   29 PHE cc_start: 0.7150 (m-80) cc_final: 0.6845 (m-10)
REVERT: H   79 TYR cc_start: 0.7258 (m-80) cc_final: 0.6617 (m-80)
REVERT: H  100 TYR cc_start: 0.7350 (p90) cc_final: 0.7138 (p90)
REVERT: L   11 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7320 (tm)
REVERT: L   18 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.6891 (tpp-160)
  outliers start: 25
  outliers final: 19
  residues processed: 106
  average time/residue: 0.0592
  time to fit residues: 7.7396
Evaluate side-chains
  108 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:    0.0050
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0770
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 2 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.3752

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
H  61 GLN
L  79 GLN
L  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.142421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.125735 restraints weight = 6931.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.129107 restraints weight = 4119.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.131472 restraints weight = 2841.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.133028 restraints weight = 2141.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.134270 restraints weight = 1733.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3356  Z= 0.123
  Angle     :  0.595   6.173   4562  Z= 0.303
  Chirality :  0.046   0.179    497
  Planarity :  0.005   0.045    589
  Dihedral  :  4.803  39.028    488
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 22.32 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.40), residues: 414
  helix: -1.40 (1.12), residues: 25
  sheet: -0.17 (0.52), residues: 88
  loop : -0.91 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 346 
 TYR   0.011   0.001   TYR H  47 
 PHE   0.009   0.001   PHE A 338 
 TRP   0.004   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3349)
  covalent geometry    : angle       0.59369 ( 4547)
  SS BOND              : bond        0.00202 (    6)
  SS BOND              : angle       0.61469 (   12)
  hydrogen bonds       : bond        0.03157 (   82)
  hydrogen bonds       : angle       6.74234 (  207)
  link_NAG-ASN         : bond        0.00260 (    1)
  link_NAG-ASN         : angle       1.31769 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.7716 (t80) cc_final: 0.7332 (t80)
REVERT: A  406 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6937 (mm-30)
REVERT: A  464 PHE cc_start: 0.6716 (t80) cc_final: 0.6232 (t80)
REVERT: H    4 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7984 (mt)
REVERT: H   29 PHE cc_start: 0.7043 (m-80) cc_final: 0.6704 (m-10)
REVERT: H   79 TYR cc_start: 0.7235 (m-80) cc_final: 0.6601 (m-80)
REVERT: H   86 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7000 (t70)
REVERT: L   11 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7205 (tm)
REVERT: L   18 ARG cc_start: 0.7652 (ttp-170) cc_final: 0.6815 (tpp-160)
  outliers start: 23
  outliers final: 11
  residues processed: 111
  average time/residue: 0.0530
  time to fit residues: 7.1368
Evaluate side-chains
  98 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   86 ASP
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   69 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 29 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 39 optimal weight:    0.4980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 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 = 0.3896 r_free = 0.3896 target = 0.140806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.124053 restraints weight = 7061.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.127342 restraints weight = 4220.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.129812 restraints weight = 2909.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.131436 restraints weight = 2178.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.132659 restraints weight = 1742.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3356  Z= 0.155
  Angle     :  0.607   5.507   4562  Z= 0.313
  Chirality :  0.047   0.193    497
  Planarity :  0.005   0.048    589
  Dihedral  :  4.890  39.563    488
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  7.63 %
    Allowed  : 20.62 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.40), residues: 414
  helix: -1.57 (1.06), residues: 25
  sheet: -0.01 (0.50), residues: 101
  loop : -0.97 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 346 
 TYR   0.016   0.002   TYR H  90 
 PHE   0.011   0.001   PHE A 338 
 TRP   0.004   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3349)
  covalent geometry    : angle       0.60515 ( 4547)
  SS BOND              : bond        0.00320 (    6)
  SS BOND              : angle       0.90677 (   12)
  hydrogen bonds       : bond        0.03516 (   82)
  hydrogen bonds       : angle       6.74274 (  207)
  link_NAG-ASN         : bond        0.00093 (    1)
  link_NAG-ASN         : angle       1.39219 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7123 (p0) cc_final: 0.6339 (t0)
REVERT: A  406 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7002 (mm-30)
REVERT: A  509 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8185 (mtp180)
REVERT: H   14 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7274 (m-80)
REVERT: H   29 PHE cc_start: 0.7132 (m-80) cc_final: 0.6717 (m-10)
REVERT: H   79 TYR cc_start: 0.7311 (m-80) cc_final: 0.6709 (m-80)
REVERT: H   86 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7214 (t70)
REVERT: L    4 MET cc_start: 0.7007 (tpp) cc_final: 0.6512 (tpp)
REVERT: L   11 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7379 (tm)
REVERT: L   18 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.6866 (tpp-160)
  outliers start: 27
  outliers final: 17
  residues processed: 104
  average time/residue: 0.0605
  time to fit residues: 7.5748
Evaluate side-chains
  104 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  509 ARG
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   14 PHE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   86 ASP
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   91 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 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 = 0.3878 r_free = 0.3878 target = 0.139143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.121980 restraints weight = 7160.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.125256 restraints weight = 4345.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.127643 restraints weight = 3024.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.129302 restraints weight = 2294.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.130471 restraints weight = 1847.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.4299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3356  Z= 0.197
  Angle     :  0.657   9.826   4562  Z= 0.338
  Chirality :  0.047   0.200    497
  Planarity :  0.005   0.044    589
  Dihedral  :  5.148  37.584    488
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  7.91 %
    Allowed  : 21.19 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.39), residues: 414
  helix: -2.04 (0.85), residues: 34
  sheet: -0.36 (0.49), residues: 95
  loop : -0.98 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 346 
 TYR   0.016   0.002   TYR A 489 
 PHE   0.012   0.002   PHE A 338 
 TRP   0.008   0.002   TRP H  36 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 3349)
  covalent geometry    : angle       0.65458 ( 4547)
  SS BOND              : bond        0.00312 (    6)
  SS BOND              : angle       1.06049 (   12)
  hydrogen bonds       : bond        0.03737 (   82)
  hydrogen bonds       : angle       6.74405 (  207)
  link_NAG-ASN         : bond        0.00000 (    1)
  link_NAG-ASN         : angle       1.51493 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7223 (p0) cc_final: 0.6551 (t0)
REVERT: A  406 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7013 (mm-30)
REVERT: H   29 PHE cc_start: 0.7191 (m-80) cc_final: 0.6638 (m-10)
REVERT: H   79 TYR cc_start: 0.7505 (m-80) cc_final: 0.6893 (m-80)
REVERT: H   86 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7281 (t70)
REVERT: L    4 MET cc_start: 0.7155 (tpp) cc_final: 0.6590 (tpp)
REVERT: L   11 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7353 (tm)
REVERT: L   18 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.6881 (tpp-160)
  outliers start: 28
  outliers final: 21
  residues processed: 106
  average time/residue: 0.0596
  time to fit residues: 7.7080
Evaluate side-chains
  107 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   14 PHE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   86 ASP
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 17 optimal weight:    0.2980
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 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 = 0.3887 r_free = 0.3887 target = 0.140169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.123094 restraints weight = 7062.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.126480 restraints weight = 4197.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.128921 restraints weight = 2885.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.130583 restraints weight = 2160.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.131775 restraints weight = 1727.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3356  Z= 0.148
  Angle     :  0.641  10.222   4562  Z= 0.325
  Chirality :  0.046   0.189    497
  Planarity :  0.005   0.044    589
  Dihedral  :  4.932  31.243    488
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  7.06 %
    Allowed  : 22.32 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.39), residues: 414
  helix: -1.74 (1.00), residues: 28
  sheet: -0.19 (0.50), residues: 100
  loop : -1.05 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 346 
 TYR   0.013   0.001   TYR A 489 
 PHE   0.016   0.001   PHE A 338 
 TRP   0.005   0.001   TRP L  35 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3349)
  covalent geometry    : angle       0.63903 ( 4547)
  SS BOND              : bond        0.00291 (    6)
  SS BOND              : angle       1.01330 (   12)
  hydrogen bonds       : bond        0.03495 (   82)
  hydrogen bonds       : angle       6.60274 (  207)
  link_NAG-ASN         : bond        0.00165 (    1)
  link_NAG-ASN         : angle       1.43262 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.7734 (t80) cc_final: 0.7105 (t80)
REVERT: A  342 PHE cc_start: 0.7216 (m-10) cc_final: 0.6960 (m-10)
REVERT: H   29 PHE cc_start: 0.7160 (m-80) cc_final: 0.6609 (m-10)
REVERT: H   79 TYR cc_start: 0.7363 (m-80) cc_final: 0.6798 (m-80)
REVERT: H   86 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7318 (t70)
REVERT: L    4 MET cc_start: 0.7156 (tpp) cc_final: 0.6722 (tpp)
REVERT: L   11 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7398 (tm)
REVERT: L   18 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.6807 (tpp-160)
  outliers start: 25
  outliers final: 20
  residues processed: 107
  average time/residue: 0.0547
  time to fit residues: 7.0879
Evaluate side-chains
  109 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue   14 PHE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   86 ASP
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0470
   chunk 21 optimal weight:    0.0370
   chunk 6 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 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 = 0.3919 r_free = 0.3919 target = 0.142565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.125671 restraints weight = 7058.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.128873 restraints weight = 4202.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.131284 restraints weight = 2934.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.132967 restraints weight = 2226.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.134206 restraints weight = 1783.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3356  Z= 0.140
  Angle     :  0.647   9.622   4562  Z= 0.328
  Chirality :  0.046   0.182    497
  Planarity :  0.005   0.043    589
  Dihedral  :  4.673  17.146    488
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 23.73 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.39), residues: 414
  helix: -1.47 (1.22), residues: 21
  sheet: -0.15 (0.50), residues: 94
  loop : -1.11 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 346 
 TYR   0.012   0.001   TYR A 489 
 PHE   0.015   0.001   PHE A 338 
 TRP   0.005   0.001   TRP L  35 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 3349)
  covalent geometry    : angle       0.64577 ( 4547)
  SS BOND              : bond        0.00294 (    6)
  SS BOND              : angle       0.85888 (   12)
  hydrogen bonds       : bond        0.03258 (   82)
  hydrogen bonds       : angle       6.52356 (  207)
  link_NAG-ASN         : bond        0.00239 (    1)
  link_NAG-ASN         : angle       1.28206 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7237 (p0) cc_final: 0.6498 (t0)
REVERT: A  449 TYR cc_start: 0.7887 (m-80) cc_final: 0.7420 (m-80)
REVERT: A  464 PHE cc_start: 0.6487 (t80) cc_final: 0.5919 (t80)
REVERT: A  465 GLU cc_start: 0.6715 (pm20) cc_final: 0.6508 (pm20)
REVERT: H   29 PHE cc_start: 0.7098 (m-80) cc_final: 0.6484 (m-10)
REVERT: H   79 TYR cc_start: 0.7291 (m-80) cc_final: 0.6758 (m-80)
REVERT: H   86 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7287 (t70)
REVERT: L    4 MET cc_start: 0.7160 (tpp) cc_final: 0.6874 (tpp)
REVERT: L   11 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7383 (tm)
REVERT: L   18 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.6822 (tpp-160)
REVERT: L   92 ASN cc_start: 0.5546 (OUTLIER) cc_final: 0.5311 (t0)
  outliers start: 24
  outliers final: 19
  residues processed: 102
  average time/residue: 0.0603
  time to fit residues: 7.4451
Evaluate side-chains
  106 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain H residue   14 PHE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   86 ASP
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue   92 ASN
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 18 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0770
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 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 = 0.3922 r_free = 0.3922 target = 0.142673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.125775 restraints weight = 6958.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.129099 restraints weight = 4151.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.131507 restraints weight = 2864.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.133056 restraints weight = 2162.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.134383 restraints weight = 1753.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.4820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3356  Z= 0.137
  Angle     :  0.656   9.574   4562  Z= 0.331
  Chirality :  0.046   0.178    497
  Planarity :  0.005   0.043    589
  Dihedral  :  4.557  16.936    487
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 23.73 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.39), residues: 414
  helix: -1.58 (1.21), residues: 20
  sheet: -0.05 (0.51), residues: 94
  loop : -1.00 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 346 
 TYR   0.011   0.001   TYR A 489 
 PHE   0.018   0.001   PHE A 338 
 TRP   0.005   0.001   TRP L  35 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3349)
  covalent geometry    : angle       0.65421 ( 4547)
  SS BOND              : bond        0.00280 (    6)
  SS BOND              : angle       0.90404 (   12)
  hydrogen bonds       : bond        0.03266 (   82)
  hydrogen bonds       : angle       6.43386 (  207)
  link_NAG-ASN         : bond        0.00250 (    1)
  link_NAG-ASN         : angle       1.30278 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  449 TYR cc_start: 0.7921 (m-80) cc_final: 0.7580 (m-80)
REVERT: A  464 PHE cc_start: 0.6508 (t80) cc_final: 0.5969 (t80)
REVERT: A  465 GLU cc_start: 0.6693 (pm20) cc_final: 0.6475 (pm20)
REVERT: H   29 PHE cc_start: 0.7083 (m-80) cc_final: 0.6472 (m-10)
REVERT: H   79 TYR cc_start: 0.7208 (m-80) cc_final: 0.6721 (m-80)
REVERT: H   86 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7297 (t70)
REVERT: L    4 MET cc_start: 0.7222 (tpp) cc_final: 0.6889 (tpp)
REVERT: L   11 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7519 (tm)
REVERT: L   18 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.6819 (tpp-160)
REVERT: L   92 ASN cc_start: 0.5565 (OUTLIER) cc_final: 0.5337 (t0)
  outliers start: 22
  outliers final: 17
  residues processed: 99
  average time/residue: 0.0758
  time to fit residues: 8.9538
Evaluate side-chains
  103 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   14 PHE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   86 ASP
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue   92 ASN
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 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 = 0.3893 r_free = 0.3893 target = 0.140655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.123832 restraints weight = 7141.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.127104 restraints weight = 4242.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.129468 restraints weight = 2939.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.131099 restraints weight = 2221.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.132310 restraints weight = 1784.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3356  Z= 0.174
  Angle     :  0.681  10.093   4562  Z= 0.348
  Chirality :  0.047   0.192    497
  Planarity :  0.005   0.044    589
  Dihedral  :  4.794  18.424    487
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 24.86 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.39), residues: 414
  helix: -1.01 (1.19), residues: 21
  sheet: -0.06 (0.51), residues: 94
  loop : -0.91 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 346 
 TYR   0.014   0.001   TYR A 489 
 PHE   0.040   0.002   PHE A 342 
 TRP   0.004   0.001   TRP A 436 
 HIS   0.000   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 3349)
  covalent geometry    : angle       0.67949 ( 4547)
  SS BOND              : bond        0.00326 (    6)
  SS BOND              : angle       0.97197 (   12)
  hydrogen bonds       : bond        0.03600 (   82)
  hydrogen bonds       : angle       6.58836 (  207)
  link_NAG-ASN         : bond        0.00140 (    1)
  link_NAG-ASN         : angle       1.20802 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 770.97 seconds
wall clock time: 13 minutes 54.25 seconds (834.25 seconds total)