Starting phenix.real_space_refine
on Wed Jun  4 15:21:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i3s_35155/06_2025/8i3s_35155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i3s_35155/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i3s_35155/06_2025/8i3s_35155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i3s_35155/06_2025/8i3s_35155.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i3s_35155/06_2025/8i3s_35155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i3s_35155/06_2025/8i3s_35155.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.41, per 1000 atoms: 1.04
  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: 0.68
  Conformation dependent library (CDL) restraints added in 361.5 milliseconds
  

  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: 0.40
  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: 0.76

  Time building geometry restraints manager: 0.84 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:             2.230
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.400
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.810
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.018   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.009   0.001   PHE A 515 
 TYR   0.010   0.001   TYR L  49 
 ARG   0.002   0.000   ARG H  50 

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

*********************** 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  : 0.337 
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: 0.7522 (t80)
REVERT: A  368 LEU cc_start: 0.5658 (mm) cc_final: 0.5449 (mm)
REVERT: A  403 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.8158 (ttp-110)
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: 0.8077 (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: 0.7202 (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: 0.6709 (mmm)
REVERT: L   18 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.6999 (tpp-160)
REVERT: L   36 TYR cc_start: 0.8654 (m-10) cc_final: 0.8420 (m-10)
REVERT: L   49 TYR cc_start: 0.8499 (p90) cc_final: 0.8092 (p90)
REVERT: L   87 TYR cc_start: 0.8368 (m-80) cc_final: 0.8127 (m-10)
  outliers start: 9
  outliers final: 3
  residues processed: 139
  average time/residue: 0.2014
  time to fit residues: 32.3516
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  : 0.402 
-------------------------------------------------------------------------------
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 33 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0020
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0770
   chunk 31 optimal weight:    0.0570
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.3664

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.140280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.124308 restraints weight = 6953.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.127567 restraints weight = 4033.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.129920 restraints weight = 2738.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3356  Z= 0.132
  Angle     :  0.576   5.292   4562  Z= 0.304
  Chirality :  0.046   0.162    497
  Planarity :  0.006   0.058    589
  Dihedral  :  4.705  39.162    490
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 16.38 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.40), residues: 414
  helix: -1.05 (0.91), residues: 31
  sheet: -0.00 (0.54), residues: 97
  loop : -0.77 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.016   0.001   PHE A 464 
 TYR   0.013   0.001   TYR A 380 
 ARG   0.004   0.001   ARG L  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00192 (    1)
  link_NAG-ASN         : angle       1.13321 (    3)
  hydrogen bonds       : bond        0.04620 (   82)
  hydrogen bonds       : angle       8.22642 (  207)
  SS BOND              : bond        0.00292 (    6)
  SS BOND              : angle       1.05112 (   12)
  covalent geometry    : bond        0.00294 ( 3349)
  covalent geometry    : angle       0.57343 ( 4547)

*********************** 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
  124 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.7834 (ttt90) cc_final: 0.6861 (ttm170)
REVERT: A  464 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.6389 (t80)
REVERT: A  474 GLN cc_start: 0.6367 (mt0) cc_final: 0.5890 (mm-40)
REVERT: A  507 PRO cc_start: 0.8167 (Cg_exo) cc_final: 0.7884 (Cg_endo)
REVERT: H   79 TYR cc_start: 0.7284 (m-80) cc_final: 0.6626 (m-80)
REVERT: L    4 MET cc_start: 0.7505 (mmm) cc_final: 0.7142 (tpp)
REVERT: L   11 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7085 (tm)
REVERT: L   18 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.6983 (tpp-160)
  outliers start: 17
  outliers final: 8
  residues processed: 113
  average time/residue: 0.1880
  time to fit residues: 24.7296
Evaluate side-chains
  107 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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 5 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0060
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3853 r_free = 0.3853 target = 0.137729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.121971 restraints weight = 7077.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.125104 restraints weight = 4223.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.127338 restraints weight = 2926.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3356  Z= 0.160
  Angle     :  0.595   6.561   4562  Z= 0.306
  Chirality :  0.046   0.178    497
  Planarity :  0.005   0.047    589
  Dihedral  :  4.882  41.027    488
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 18.36 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.40), residues: 414
  helix: -0.89 (0.97), residues: 31
  sheet: -0.19 (0.52), residues: 96
  loop : -0.76 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 353 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.015   0.001   PHE A 338 
 TYR   0.012   0.001   TYR H  47 
 ARG   0.004   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00141 (    1)
  link_NAG-ASN         : angle       1.26622 (    3)
  hydrogen bonds       : bond        0.03904 (   82)
  hydrogen bonds       : angle       7.31437 (  207)
  SS BOND              : bond        0.00245 (    6)
  SS BOND              : angle       0.80738 (   12)
  covalent geometry    : bond        0.00360 ( 3349)
  covalent geometry    : angle       0.59350 ( 4547)

*********************** 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: 22
    poor density    : 99
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.8261 (ttt90) cc_final: 0.6841 (ttm170)
REVERT: A  464 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.6063 (t80)
REVERT: A  474 GLN cc_start: 0.6286 (mt0) cc_final: 0.5830 (mm-40)
REVERT: H   79 TYR cc_start: 0.7248 (m-80) cc_final: 0.6652 (m-80)
REVERT: L    4 MET cc_start: 0.7531 (mmm) cc_final: 0.6840 (mmm)
REVERT: L   11 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7109 (tm)
REVERT: L   18 ARG cc_start: 0.7763 (ttp-170) cc_final: 0.6926 (tpp-160)
  outliers start: 22
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1912
  time to fit residues: 24.6643
Evaluate side-chains
  106 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
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 A residue  524 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   30 SER
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   69 THR
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 34 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0020
   chunk 12 optimal weight:    0.2980
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.141284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.124668 restraints weight = 6980.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.127979 restraints weight = 4177.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.130322 restraints weight = 2907.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.3590

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= 0.131
  Angle     :  0.573   5.489   4562  Z= 0.291
  Chirality :  0.046   0.181    497
  Planarity :  0.005   0.045    589
  Dihedral  :  4.782  40.086    488
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 19.77 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.41), residues: 414
  helix: -0.62 (1.14), residues: 25
  sheet: -0.05 (0.52), residues: 94
  loop : -0.67 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H 103 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.006   0.001   PHE A 464 
 TYR   0.014   0.001   TYR H  47 
 ARG   0.005   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00212 (    1)
  link_NAG-ASN         : angle       1.27549 (    3)
  hydrogen bonds       : bond        0.03384 (   82)
  hydrogen bonds       : angle       6.92886 (  207)
  SS BOND              : bond        0.00228 (    6)
  SS BOND              : angle       0.67965 (   12)
  covalent geometry    : bond        0.00296 ( 3349)
  covalent geometry    : angle       0.57204 ( 4547)

*********************** 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: 24
    poor density    : 96
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  457 ARG cc_start: 0.7613 (ttt-90) cc_final: 0.7347 (ttt90)
REVERT: A  464 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5972 (t80)
REVERT: A  474 GLN cc_start: 0.6361 (mt0) cc_final: 0.5852 (mm-40)
REVERT: H   29 PHE cc_start: 0.7061 (m-10) cc_final: 0.6534 (m-10)
REVERT: H   79 TYR cc_start: 0.7247 (m-80) cc_final: 0.6627 (m-80)
REVERT: H   86 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7198 (t70)
REVERT: L   11 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7135 (tm)
REVERT: L   18 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.6844 (tpp-160)
  outliers start: 24
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1606
  time to fit residues: 21.2948
Evaluate side-chains
  104 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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    6 GLN
Chi-restraints excluded: chain H residue   30 SER
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   96 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    0.0670
   chunk 20 optimal weight:    3.9990
   chunk 2 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3909 r_free = 0.3909 target = 0.141828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.124913 restraints weight = 7068.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.128242 restraints weight = 4260.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.130649 restraints weight = 2965.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.3862

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= 0.131
  Angle     :  0.587   5.519   4562  Z= 0.298
  Chirality :  0.046   0.180    497
  Planarity :  0.005   0.043    589
  Dihedral  :  4.763  39.475    488
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 21.19 %
    Favored  : 72.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.41), residues: 414
  helix: -0.66 (1.13), residues: 25
  sheet: -0.12 (0.51), residues: 88
  loop : -0.69 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H 103 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.008   0.001   PHE A 338 
 TYR   0.012   0.001   TYR A 423 
 ARG   0.006   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00239 (    1)
  link_NAG-ASN         : angle       1.25694 (    3)
  hydrogen bonds       : bond        0.03238 (   82)
  hydrogen bonds       : angle       6.73460 (  207)
  SS BOND              : bond        0.00212 (    6)
  SS BOND              : angle       0.59407 (   12)
  covalent geometry    : bond        0.00300 ( 3349)
  covalent geometry    : angle       0.58586 ( 4547)

*********************** 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
  114 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.7818 (t80) cc_final: 0.7422 (t80)
REVERT: A  457 ARG cc_start: 0.7614 (ttt-90) cc_final: 0.7257 (ttt90)
REVERT: H   79 TYR cc_start: 0.7284 (m-80) cc_final: 0.6674 (m-80)
REVERT: L   11 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7102 (tm)
REVERT: L   18 ARG cc_start: 0.7670 (ttp-170) cc_final: 0.6835 (tpp-160)
  outliers start: 22
  outliers final: 15
  residues processed: 104
  average time/residue: 0.1652
  time to fit residues: 20.6247
Evaluate side-chains
  101 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
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  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   30 SER
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   74 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.138959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.122166 restraints weight = 7096.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.125432 restraints weight = 4225.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.127729 restraints weight = 2916.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.4032

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= 0.171
  Angle     :  0.603   5.807   4562  Z= 0.311
  Chirality :  0.046   0.189    497
  Planarity :  0.005   0.043    589
  Dihedral  :  4.940  39.986    488
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 22.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.40), residues: 414
  helix: -0.28 (1.28), residues: 19
  sheet: -0.10 (0.51), residues: 95
  loop : -0.87 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.012   0.001   PHE A 338 
 TYR   0.012   0.001   TYR A 489 
 ARG   0.006   0.001   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00104 (    1)
  link_NAG-ASN         : angle       1.37462 (    3)
  hydrogen bonds       : bond        0.03545 (   82)
  hydrogen bonds       : angle       6.77313 (  207)
  SS BOND              : bond        0.00270 (    6)
  SS BOND              : angle       0.80245 (   12)
  covalent geometry    : bond        0.00388 ( 3349)
  covalent geometry    : angle       0.60200 ( 4547)

*********************** 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: 24
    poor density    : 89
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7219 (p0) cc_final: 0.6448 (t0)
REVERT: A  457 ARG cc_start: 0.7667 (ttt-90) cc_final: 0.7451 (ttt-90)
REVERT: A  509 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8269 (mtp180)
REVERT: H   79 TYR cc_start: 0.7364 (m-80) cc_final: 0.6712 (m-80)
REVERT: L    4 MET cc_start: 0.6916 (tpp) cc_final: 0.6457 (tpp)
REVERT: L   11 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7274 (tm)
REVERT: L   18 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.6874 (tpp-160)
  outliers start: 24
  outliers final: 19
  residues processed: 105
  average time/residue: 0.1708
  time to fit residues: 21.3302
Evaluate side-chains
  106 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
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   30 SER
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    7 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0870
   chunk 16 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 34 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.140891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.124178 restraints weight = 6955.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.127326 restraints weight = 4210.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.129627 restraints weight = 2951.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3356  Z= 0.153
  Angle     :  0.608   8.674   4562  Z= 0.312
  Chirality :  0.047   0.216    497
  Planarity :  0.005   0.071    589
  Dihedral  :  4.873  35.422    488
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 24.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.40), residues: 414
  helix: -0.92 (1.20), residues: 21
  sheet: -0.15 (0.50), residues: 95
  loop : -0.90 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP H 103 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.014   0.001   PHE A 338 
 TYR   0.019   0.002   TYR H  90 
 ARG   0.007   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00196 (    1)
  link_NAG-ASN         : angle       1.35709 (    3)
  hydrogen bonds       : bond        0.03540 (   82)
  hydrogen bonds       : angle       6.72797 (  207)
  SS BOND              : bond        0.00263 (    6)
  SS BOND              : angle       0.67128 (   12)
  covalent geometry    : bond        0.00350 ( 3349)
  covalent geometry    : angle       0.60693 ( 4547)

*********************** 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
  109 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  457 ARG cc_start: 0.7551 (ttt-90) cc_final: 0.7216 (ttt90)
REVERT: H   79 TYR cc_start: 0.7294 (m-80) cc_final: 0.6711 (m-80)
REVERT: H   86 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7171 (t70)
REVERT: L    4 MET cc_start: 0.7038 (tpp) cc_final: 0.6540 (tpp)
REVERT: L   11 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7263 (tm)
REVERT: L   18 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.6857 (tpp-160)
  outliers start: 22
  outliers final: 18
  residues processed: 102
  average time/residue: 0.1812
  time to fit residues: 22.0694
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  : 0.351 
-------------------------------------------------------------------------------
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  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   30 SER
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   61 ARG
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 15 optimal weight:    0.4980
   chunk 1 optimal weight:    0.0770
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.141196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.124435 restraints weight = 7035.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.127671 restraints weight = 4215.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.129993 restraints weight = 2937.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.4292

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= 0.145
  Angle     :  0.610   9.321   4562  Z= 0.312
  Chirality :  0.046   0.193    497
  Planarity :  0.005   0.060    589
  Dihedral  :  4.832  31.259    488
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 24.58 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.40), residues: 414
  helix: -0.97 (1.19), residues: 21
  sheet: -0.18 (0.51), residues: 95
  loop : -0.93 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.016   0.001   PHE A 338 
 TYR   0.012   0.001   TYR A 489 
 ARG   0.008   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00201 (    1)
  link_NAG-ASN         : angle       1.37035 (    3)
  hydrogen bonds       : bond        0.03497 (   82)
  hydrogen bonds       : angle       6.62908 (  207)
  SS BOND              : bond        0.00289 (    6)
  SS BOND              : angle       0.74410 (   12)
  covalent geometry    : bond        0.00334 ( 3349)
  covalent geometry    : angle       0.60866 ( 4547)

*********************** 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
  112 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.7809 (t80) cc_final: 0.7123 (t80)
REVERT: A  342 PHE cc_start: 0.7218 (m-10) cc_final: 0.7006 (m-10)
REVERT: A  394 ASN cc_start: 0.7256 (p0) cc_final: 0.6506 (t0)
REVERT: A  457 ARG cc_start: 0.7598 (ttt-90) cc_final: 0.7203 (ttt90)
REVERT: H   79 TYR cc_start: 0.7409 (m-80) cc_final: 0.6799 (m-80)
REVERT: H   86 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7216 (t70)
REVERT: L    4 MET cc_start: 0.7073 (tpp) cc_final: 0.6562 (tpp)
REVERT: L   11 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7367 (tm)
REVERT: L   18 ARG cc_start: 0.7668 (ttp-170) cc_final: 0.6795 (tpp-160)
  outliers start: 22
  outliers final: 19
  residues processed: 105
  average time/residue: 0.1650
  time to fit residues: 20.8116
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  : 0.339 
-------------------------------------------------------------------------------
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  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   30 SER
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   61 ARG
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 15 optimal weight:    0.3980
   chunk 21 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.139929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.123299 restraints weight = 7048.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.126415 restraints weight = 4261.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.128658 restraints weight = 3000.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.4371

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     :  0.637  10.201   4562  Z= 0.327
  Chirality :  0.047   0.195    497
  Planarity :  0.005   0.058    589
  Dihedral  :  4.846  20.111    488
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 24.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.39), residues: 414
  helix: -0.98 (1.19), residues: 21
  sheet: -0.24 (0.50), residues: 95
  loop : -1.02 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.014   0.002   PHE A 338 
 TYR   0.014   0.001   TYR A 489 
 ARG   0.008   0.001   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    1)
  link_NAG-ASN         : angle       1.37731 (    3)
  hydrogen bonds       : bond        0.03622 (   82)
  hydrogen bonds       : angle       6.72630 (  207)
  SS BOND              : bond        0.00324 (    6)
  SS BOND              : angle       0.76794 (   12)
  covalent geometry    : bond        0.00400 ( 3349)
  covalent geometry    : angle       0.63539 ( 4547)

*********************** 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
  109 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.7836 (t80) cc_final: 0.7153 (t80)
REVERT: A  394 ASN cc_start: 0.7313 (p0) cc_final: 0.6635 (t0)
REVERT: A  509 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8285 (mtp180)
REVERT: H   79 TYR cc_start: 0.7245 (m-80) cc_final: 0.6630 (m-80)
REVERT: L    4 MET cc_start: 0.7132 (tpp) cc_final: 0.6679 (tpp)
REVERT: L   11 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7346 (tm)
REVERT: L   18 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.6866 (tpp-160)
  outliers start: 22
  outliers final: 20
  residues processed: 100
  average time/residue: 0.1748
  time to fit residues: 20.9914
Evaluate side-chains
  107 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
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  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  509 ARG
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   30 SER
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 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   96 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 15 optimal weight:    0.0870
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0270
   chunk 8 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.4616

-------------------------------------------------------------------------------
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
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.141102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.124454 restraints weight = 6929.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.127642 restraints weight = 4170.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.129993 restraints weight = 2917.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.4486

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     :  0.636   9.952   4562  Z= 0.325
  Chirality :  0.046   0.186    497
  Planarity :  0.005   0.055    589
  Dihedral  :  4.686  20.564    487
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 24.86 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.40), residues: 414
  helix: -1.10 (1.17), residues: 21
  sheet: -0.14 (0.51), residues: 95
  loop : -0.98 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 436 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.026   0.001   PHE A 338 
 TYR   0.012   0.001   TYR A 489 
 ARG   0.008   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00275 (    1)
  link_NAG-ASN         : angle       1.47936 (    3)
  hydrogen bonds       : bond        0.03646 (   82)
  hydrogen bonds       : angle       6.63784 (  207)
  SS BOND              : bond        0.00336 (    6)
  SS BOND              : angle       0.64750 (   12)
  covalent geometry    : bond        0.00322 ( 3349)
  covalent geometry    : angle       0.63532 ( 4547)

********************** 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
  105 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8370 (mtp180)
REVERT: H   79 TYR cc_start: 0.7373 (m-80) cc_final: 0.6741 (m-80)
REVERT: L    4 MET cc_start: 0.7138 (tpp) cc_final: 0.6750 (tpp)
REVERT: L    6 GLN cc_start: 0.6695 (tt0) cc_final: 0.6447 (tt0)
REVERT: L   11 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7333 (tm)
REVERT: L   18 ARG cc_start: 0.7684 (ttp-170) cc_final: 0.6772 (tpp-160)
  outliers start: 19
  outliers final: 15
  residues processed: 100
  average time/residue: 0.1797
  time to fit residues: 21.3964
Evaluate side-chains
  97 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  509 ARG
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   30 SER
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 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   96 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    0.3980
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 37 optimal weight:    0.4980
   chunk 23 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0270
   chunk 1 optimal weight:    0.7980
   chunk 25 optimal weight:    0.3980
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
L  37 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.143124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.126594 restraints weight = 7046.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.129822 restraints weight = 4180.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.132096 restraints weight = 2909.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.4713

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= 0.135
  Angle     :  0.662   9.495   4562  Z= 0.337
  Chirality :  0.047   0.173    497
  Planarity :  0.005   0.054    589
  Dihedral  :  4.652  20.751    487
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 24.86 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.40), residues: 414
  helix: -1.14 (1.16), residues: 20
  sheet: -0.11 (0.51), residues: 95
  loop : -0.94 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 436 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.032   0.002   PHE A 338 
 TYR   0.012   0.001   TYR H  79 
 ARG   0.008   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00288 (    1)
  link_NAG-ASN         : angle       1.24906 (    3)
  hydrogen bonds       : bond        0.03502 (   82)
  hydrogen bonds       : angle       6.56731 (  207)
  SS BOND              : bond        0.00296 (    6)
  SS BOND              : angle       0.80385 (   12)
  covalent geometry    : bond        0.00319 ( 3349)
  covalent geometry    : angle       0.66053 ( 4547)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1751.57 seconds
wall clock time: 31 minutes 13.88 seconds (1873.88 seconds total)