Starting phenix.real_space_refine
on Sat Apr 26 23:55:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z86_39839/04_2025/8z86_39839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z86_39839/04_2025/8z86_39839.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z86_39839/04_2025/8z86_39839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z86_39839/04_2025/8z86_39839.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z86_39839/04_2025/8z86_39839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z86_39839/04_2025/8z86_39839.cif"
  }
  resolution = 3.87
  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=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 820 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2043      2.51       5
     N     552      2.21       5
     O     608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3219
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1540
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 12, 'TRANS': 180}
    Chain: "H"
      Number of atoms: 863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 863
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "L"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 816
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100}
  Time building chain proxies: 2.77, per 1000 atoms: 0.86
  Number of scatterers: 3219
  At special positions: 0
  Unit cell: (67.6, 75.92, 86.32, 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     608      8.00
     N     552      7.00
     C    2043      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 334 " - pdb=" SG  CYS A 359 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 377 " - pdb=" SG  CYS A 430 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 523 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 478 " - pdb=" SG  CYS A 486 " distance=2.01
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.04

  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
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 389.2 milliseconds
  

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  752

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 7 sheets defined
      6.7% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 363 through 367
      removed outlier: 4.118A  pdb=" N   TYR A 367 " --> pdb=" O   SER A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 409
      removed outlier: 3.523A  pdb=" N   VAL A 405 " --> pdb=" O   GLY A 402 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   SER A 406 " --> pdb=" O   ASN A 403 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   GLN A 407 " --> pdb=" O   GLU A 404 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ILE A 408 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ALA A 409 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 419
    Processing helix  chain 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.059A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 352 through 355
      removed outlier: 3.830A  pdb=" N   VAL A 510 " --> pdb=" O   ASP A 396 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A 508 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU A 511 " --> pdb=" O   CYS A 430 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 450 through 451
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.583A  pdb=" N   GLN H 110 " --> pdb=" O   TYR H  93 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   SER H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 19 through 22
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7
      removed outlier: 4.062A  pdb=" N   SER L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.596A  pdb=" N   LEU L  11 " --> pdb=" O   ARG L 104 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLU L 106 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 34 through 39

    60 hydrogen bonds defined for protein.
    141 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: 0.74

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 521
        1.32 -     1.44: 983
        1.44 -     1.57: 1775
        1.57 -     1.70: 2
        1.70 -     1.82: 20
  Bond restraints: 3301
  Sorted by residual:
  bond pdb=" C   PHE A 488 "
       pdb=" O   PHE A 488 "
    ideal  model  delta    sigma   weight residual
    1.238  1.191  0.046 1.28e-02 6.10e+03 1.31e+01
  bond pdb=" N   CYS A 486 "
       pdb=" CA  CYS A 486 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.18e-02 7.18e+03 9.23e+00
  bond pdb=" CA  ALA A 482 "
       pdb=" CB  ALA A 482 "
    ideal  model  delta    sigma   weight residual
    1.530  1.481  0.050 1.69e-02 3.50e+03 8.59e+00
  bond pdb=" N   VAL A 484 "
       pdb=" CA  VAL A 484 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.19e-02 7.06e+03 7.80e+00
  bond pdb=" CB  PRO H  87 "
       pdb=" CG  PRO H  87 "
    ideal  model  delta    sigma   weight residual
    1.492  1.624 -0.132 5.00e-02 4.00e+02 6.94e+00
  ... (remaining 3296 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.79: 4454
        4.79 -     9.59: 27
        9.59 -    14.38: 5
       14.38 -    19.18: 0
       19.18 -    23.97: 1
  Bond angle restraints: 4487
  Sorted by residual:
  angle pdb=" N   TYR A 487 "
        pdb=" CA  TYR A 487 "
        pdb=" CB  TYR A 487 "
      ideal   model   delta    sigma   weight residual
     111.53   87.56   23.97 1.86e+00 2.89e-01 1.66e+02
  angle pdb=" CA  PRO H  87 "
        pdb=" N   PRO H  87 "
        pdb=" CD  PRO H  87 "
      ideal   model   delta    sigma   weight residual
     112.00   98.92   13.08 1.40e+00 5.10e-01 8.73e+01
  angle pdb=" CA  PRO H  14 "
        pdb=" N   PRO H  14 "
        pdb=" CD  PRO H  14 "
      ideal   model   delta    sigma   weight residual
     112.00  101.96   10.04 1.40e+00 5.10e-01 5.14e+01
  angle pdb=" CA  TYR A 487 "
        pdb=" C   TYR A 487 "
        pdb=" O   TYR A 487 "
      ideal   model   delta    sigma   weight residual
     121.06  113.59    7.47 1.16e+00 7.43e-01 4.15e+01
  angle pdb=" C   ASN A 485 "
        pdb=" CA  ASN A 485 "
        pdb=" CB  ASN A 485 "
      ideal   model   delta    sigma   weight residual
     111.73  119.41   -7.68 1.42e+00 4.96e-01 2.93e+01
  ... (remaining 4482 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.91: 1589
       15.91 -    31.83: 253
       31.83 -    47.74: 74
       47.74 -    63.65: 24
       63.65 -    79.57: 2
  Dihedral angle restraints: 1942
    sinusoidal: 752
      harmonic: 1190
  Sorted by residual:
  dihedral pdb=" N   TYR A 487 "
           pdb=" C   TYR A 487 "
           pdb=" CA  TYR A 487 "
           pdb=" CB  TYR A 487 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   96.12   26.68     0      2.50e+00 1.60e-01 1.14e+02
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  95 "
           pdb=" CB  CYS H  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.76   51.24     1      1.00e+01 1.00e-02 3.59e+01
  dihedral pdb=" CA  PHE A 398 "
           pdb=" C   PHE A 398 "
           pdb=" N   VAL A 399 "
           pdb=" CA  VAL A 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.10   29.90     0      5.00e+00 4.00e-02 3.58e+01
  ... (remaining 1939 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 364
       0.056 -    0.112: 91
       0.112 -    0.168: 17
       0.168 -    0.224: 3
       0.224 -    0.280: 3
  Chirality restraints: 478
  Sorted by residual:
  chirality pdb=" CA  TYR A 487 "
            pdb=" N   TYR A 487 "
            pdb=" C   TYR A 487 "
            pdb=" CB  TYR A 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  PRO H  14 "
            pdb=" N   PRO H  14 "
            pdb=" C   PRO H  14 "
            pdb=" CB  PRO H  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  PRO H  87 "
            pdb=" N   PRO H  87 "
            pdb=" C   PRO H  87 "
            pdb=" CB  PRO H  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 475 not shown)

  Planarity restraints: 586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  47 "    0.029 2.00e-02 2.50e+03   2.99e-02 2.24e+01
        pdb=" CG  TRP H  47 "   -0.076 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  47 "    0.046 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  47 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  47 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  47 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  47 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN H  13 "   -0.079 5.00e-02 4.00e+02   1.13e-01 2.04e+01
        pdb=" N   PRO H  14 "    0.195 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 481 "    0.023 2.00e-02 2.50e+03   4.48e-02 2.01e+01
        pdb=" C   VAL A 481 "   -0.078 2.00e-02 2.50e+03
        pdb=" O   VAL A 481 "    0.029 2.00e-02 2.50e+03
        pdb=" N   ALA A 482 "    0.026 2.00e-02 2.50e+03
  ... (remaining 583 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1001
        2.82 -     3.34: 2605
        3.34 -     3.86: 5032
        3.86 -     4.38: 5474
        4.38 -     4.90: 9748
  Nonbonded interactions: 23860
  Sorted by model distance:
  nonbonded pdb=" O   SER H   7 "
            pdb=" OG  SER H  21 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" N   ASP H  61 "
            pdb=" OD1 ASP H  61 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" NH2 ARG A 401 "
            pdb=" OE2 GLU A 404 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OG  SER A 467 "
            pdb=" OE1 GLU A 469 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" NE  ARG A 452 "
            pdb=" OD2 ASP A 465 "
     model   vdw
     2.371 3.120
  ... (remaining 23855 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:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.650
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:3.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
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      :  0.005   0.132   3307  Z= 0.238
  Angle     :  1.064  23.974   4499  Z= 0.582
  Chirality :  0.055   0.280    478
  Planarity :  0.009   0.113    586
  Dihedral  : 17.269  79.565   1172
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.33 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 35.07 %
    Favored  : 64.35 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.85 (0.39), residues: 409
  helix: -3.62 (0.89), residues: 15
  sheet: -1.33 (0.49), residues: 127
  loop : -2.18 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.076   0.005   TRP H  47 
 HIS   0.001   0.001   HIS A 517 
 PHE   0.023   0.002   PHE L  72 
 TYR   0.019   0.002   TYR L  37 
 ARG   0.005   0.001   ARG L  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28400 (   60)
  hydrogen bonds       : angle      11.62370 (  141)
  SS BOND              : bond        0.00807 (    6)
  SS BOND              : angle       2.62605 (   12)
  covalent geometry    : bond        0.00541 ( 3301)
  covalent geometry    : angle       1.05648 ( 4487)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.373 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 74
  average time/residue: 0.1423
  time to fit residues: 12.9768
Evaluate side-chains
  72 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain H residue   39 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 16 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0980
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 475 ASN
A 485 ASN
H   6 GLN
H  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.174119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.150084 restraints weight = 4387.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.151853 restraints weight = 3488.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.153507 restraints weight = 2999.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3307  Z= 0.152
  Angle     :  0.636   8.519   4499  Z= 0.325
  Chirality :  0.043   0.122    478
  Planarity :  0.005   0.058    586
  Dihedral  :  5.201  25.651    466
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 30.72 %
    Favored  : 64.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.64 (0.41), residues: 409
  helix: -3.50 (1.19), residues: 15
  sheet: -1.20 (0.48), residues: 139
  loop : -2.03 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP H  47 
 HIS   0.000   0.000   HIS H  72 
 PHE   0.008   0.001   PHE H  67 
 TYR   0.016   0.001   TYR L  37 
 ARG   0.003   0.000   ARG H  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03878 (   60)
  hydrogen bonds       : angle       7.16871 (  141)
  SS BOND              : bond        0.00576 (    6)
  SS BOND              : angle       1.26157 (   12)
  covalent geometry    : bond        0.00366 ( 3301)
  covalent geometry    : angle       0.63363 ( 4487)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  466 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7244 (pp)
REVERT: H   92 MET cc_start: 0.7918 (ttm) cc_final: 0.7702 (ttm)
  outliers start: 18
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1492
  time to fit residues: 15.3559
Evaluate side-chains
  78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   chunk 8 optimal weight:    0.2980
   chunk 36 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 475 ASN
H   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.162049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.137225 restraints weight = 4502.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.136235 restraints weight = 4028.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.136898 restraints weight = 4279.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3307  Z= 0.162
  Angle     :  0.633   8.804   4499  Z= 0.319
  Chirality :  0.043   0.124    478
  Planarity :  0.004   0.042    586
  Dihedral  :  5.112  30.276    463
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 29.28 %
    Favored  : 64.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.67 (0.41), residues: 409
  helix: -3.70 (1.01), residues: 15
  sheet: -1.33 (0.47), residues: 142
  loop : -1.97 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP H  47 
 HIS   0.001   0.000   HIS H  72 
 PHE   0.010   0.002   PHE L  72 
 TYR   0.012   0.001   TYR L  37 
 ARG   0.002   0.000   ARG H  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (   60)
  hydrogen bonds       : angle       6.61641 (  141)
  SS BOND              : bond        0.00510 (    6)
  SS BOND              : angle       1.17022 (   12)
  covalent geometry    : bond        0.00388 ( 3301)
  covalent geometry    : angle       0.63089 ( 4487)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: A  466 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7315 (pp)
REVERT: H   92 MET cc_start: 0.7905 (ttm) cc_final: 0.7681 (ttm)
REVERT: L   37 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6670 (p90)
REVERT: L   50 TYR cc_start: 0.8000 (p90) cc_final: 0.7676 (p90)
  outliers start: 20
  outliers final: 16
  residues processed: 86
  average time/residue: 0.1355
  time to fit residues: 14.4487
Evaluate side-chains
  83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  103 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 12 optimal weight:    0.4980
   chunk 1 optimal weight:    0.2980
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
H   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.157659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.131269 restraints weight = 4565.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.130208 restraints weight = 3765.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.130476 restraints weight = 4080.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3307  Z= 0.121
  Angle     :  0.598   7.839   4499  Z= 0.301
  Chirality :  0.042   0.124    478
  Planarity :  0.004   0.034    586
  Dihedral  :  4.877  28.193    463
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 29.57 %
    Favored  : 64.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.55 (0.40), residues: 409
  helix: -3.71 (0.98), residues: 15
  sheet: -0.96 (0.50), residues: 126
  loop : -2.04 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP H  47 
 HIS   0.001   0.000   HIS A 503 
 PHE   0.007   0.001   PHE L  72 
 TYR   0.011   0.001   TYR L  37 
 ARG   0.003   0.000   ARG H  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03153 (   60)
  hydrogen bonds       : angle       6.20922 (  141)
  SS BOND              : bond        0.00455 (    6)
  SS BOND              : angle       1.01398 (   12)
  covalent geometry    : bond        0.00291 ( 3301)
  covalent geometry    : angle       0.59619 ( 4487)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7604 (p0) cc_final: 0.7127 (p0)
REVERT: A  466 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7208 (pp)
REVERT: H   92 MET cc_start: 0.7904 (ttm) cc_final: 0.7632 (ttm)
REVERT: L   50 TYR cc_start: 0.8032 (p90) cc_final: 0.7742 (p90)
  outliers start: 21
  outliers final: 17
  residues processed: 81
  average time/residue: 0.1387
  time to fit residues: 14.4468
Evaluate side-chains
  83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    0.0970
   chunk 9 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0980
   chunk 38 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
H  76 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.175751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.151326 restraints weight = 4427.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.153226 restraints weight = 3547.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.154771 restraints weight = 3055.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3307  Z= 0.106
  Angle     :  0.595   8.684   4499  Z= 0.296
  Chirality :  0.042   0.122    478
  Planarity :  0.004   0.031    586
  Dihedral  :  4.574  24.026    463
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 31.59 %
    Favored  : 62.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.49 (0.40), residues: 409
  helix: -3.64 (0.95), residues: 15
  sheet: -1.02 (0.49), residues: 126
  loop : -1.94 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP H  47 
 HIS   0.001   0.000   HIS H  72 
 PHE   0.012   0.001   PHE A 390 
 TYR   0.011   0.001   TYR L  37 
 ARG   0.003   0.000   ARG H  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02921 (   60)
  hydrogen bonds       : angle       5.95623 (  141)
  SS BOND              : bond        0.00417 (    6)
  SS BOND              : angle       0.94430 (   12)
  covalent geometry    : bond        0.00253 ( 3301)
  covalent geometry    : angle       0.59345 ( 4487)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7699 (p0) cc_final: 0.7376 (p0)
REVERT: A  466 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7169 (pp)
REVERT: H   22 CYS cc_start: 0.6953 (t) cc_final: 0.6637 (t)
REVERT: H   92 MET cc_start: 0.7806 (ttm) cc_final: 0.7498 (ttm)
REVERT: L   50 TYR cc_start: 0.8051 (p90) cc_final: 0.7722 (p90)
  outliers start: 21
  outliers final: 14
  residues processed: 84
  average time/residue: 0.1160
  time to fit residues: 12.5551
Evaluate side-chains
  80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   55 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 6 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.172353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.147096 restraints weight = 4518.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.148932 restraints weight = 3624.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.150509 restraints weight = 3107.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3307  Z= 0.146
  Angle     :  0.626   8.674   4499  Z= 0.313
  Chirality :  0.042   0.121    478
  Planarity :  0.004   0.031    586
  Dihedral  :  4.739  29.144    463
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 31.30 %
    Favored  : 62.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.41 (0.40), residues: 409
  helix: -3.68 (0.94), residues: 15
  sheet: -0.96 (0.50), residues: 126
  loop : -1.88 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP H  47 
 HIS   0.000   0.000   HIS H  72 
 PHE   0.015   0.002   PHE A 369 
 TYR   0.018   0.001   TYR A 378 
 ARG   0.002   0.000   ARG H  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03099 (   60)
  hydrogen bonds       : angle       5.87164 (  141)
  SS BOND              : bond        0.00449 (    6)
  SS BOND              : angle       0.96309 (   12)
  covalent geometry    : bond        0.00352 ( 3301)
  covalent geometry    : angle       0.62479 ( 4487)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7644 (p0) cc_final: 0.7210 (p0)
REVERT: A  466 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7219 (pp)
REVERT: H   22 CYS cc_start: 0.6979 (t) cc_final: 0.6764 (t)
REVERT: H   92 MET cc_start: 0.7813 (ttm) cc_final: 0.7530 (ttm)
REVERT: L   37 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6624 (p90)
REVERT: L   50 TYR cc_start: 0.8067 (p90) cc_final: 0.7765 (p90)
  outliers start: 23
  outliers final: 18
  residues processed: 87
  average time/residue: 0.1210
  time to fit residues: 13.4385
Evaluate side-chains
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.3980
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0970
   chunk 14 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 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 = 0.4011 r_free = 0.4011 target = 0.174589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.149560 restraints weight = 4469.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.151481 restraints weight = 3609.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.152764 restraints weight = 3113.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3307  Z= 0.138
  Angle     :  0.641   9.098   4499  Z= 0.317
  Chirality :  0.043   0.122    478
  Planarity :  0.004   0.032    586
  Dihedral  :  4.793  30.379    463
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 31.30 %
    Favored  : 62.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.41 (0.40), residues: 409
  helix: -3.73 (0.92), residues: 15
  sheet: -1.06 (0.51), residues: 121
  loop : -1.81 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.067   0.003   TRP H  47 
 HIS   0.000   0.000   HIS A 503 
 PHE   0.012   0.001   PHE A 390 
 TYR   0.014   0.001   TYR A 378 
 ARG   0.002   0.000   ARG H  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03038 (   60)
  hydrogen bonds       : angle       5.86343 (  141)
  SS BOND              : bond        0.00446 (    6)
  SS BOND              : angle       1.49411 (   12)
  covalent geometry    : bond        0.00332 ( 3301)
  covalent geometry    : angle       0.63678 ( 4487)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7687 (p0) cc_final: 0.7240 (p0)
REVERT: A  466 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7203 (pp)
REVERT: H   22 CYS cc_start: 0.6950 (t) cc_final: 0.6741 (t)
REVERT: H   92 MET cc_start: 0.7817 (ttm) cc_final: 0.7532 (ttm)
REVERT: L   37 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6737 (p90)
REVERT: L   50 TYR cc_start: 0.8076 (p90) cc_final: 0.7811 (p90)
  outliers start: 23
  outliers final: 19
  residues processed: 85
  average time/residue: 0.1209
  time to fit residues: 13.0564
Evaluate side-chains
  84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 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 = 0.3718 r_free = 0.3718 target = 0.153501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.126278 restraints weight = 4686.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.124342 restraints weight = 5149.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.124831 restraints weight = 4964.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3307  Z= 0.156
  Angle     :  0.661   9.420   4499  Z= 0.328
  Chirality :  0.043   0.123    478
  Planarity :  0.004   0.033    586
  Dihedral  :  4.979  34.203    463
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  7.25 %
    Allowed  : 30.72 %
    Favored  : 62.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.37 (0.40), residues: 409
  helix: -3.71 (0.92), residues: 15
  sheet: -0.90 (0.49), residues: 125
  loop : -1.87 (0.35), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.003   TRP H  47 
 HIS   0.000   0.000   HIS A 503 
 PHE   0.007   0.001   PHE L  72 
 TYR   0.016   0.001   TYR A 506 
 ARG   0.003   0.000   ARG H  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03161 (   60)
  hydrogen bonds       : angle       5.88048 (  141)
  SS BOND              : bond        0.00467 (    6)
  SS BOND              : angle       1.97632 (   12)
  covalent geometry    : bond        0.00377 ( 3301)
  covalent geometry    : angle       0.65347 ( 4487)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7679 (p0) cc_final: 0.7254 (p0)
REVERT: A  466 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7171 (pp)
REVERT: H   22 CYS cc_start: 0.6950 (t) cc_final: 0.6739 (t)
REVERT: H   92 MET cc_start: 0.7856 (ttm) cc_final: 0.7577 (ttm)
REVERT: L   37 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6785 (p90)
REVERT: L   50 TYR cc_start: 0.8065 (p90) cc_final: 0.7796 (p90)
  outliers start: 25
  outliers final: 20
  residues processed: 85
  average time/residue: 0.1181
  time to fit residues: 12.9760
Evaluate side-chains
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  420 ASN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 20 optimal weight:    0.0270
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0970
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5236

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 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 = 0.4011 r_free = 0.4011 target = 0.174755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.148537 restraints weight = 4532.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.150507 restraints weight = 3540.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.152402 restraints weight = 3019.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3307  Z= 0.123
  Angle     :  0.652  10.857   4499  Z= 0.321
  Chirality :  0.043   0.125    478
  Planarity :  0.004   0.032    586
  Dihedral  :  4.804  29.705    463
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 31.59 %
    Favored  : 62.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.25 (0.40), residues: 409
  helix: -3.66 (0.93), residues: 15
  sheet: -0.82 (0.49), residues: 125
  loop : -1.77 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP H  47 
 HIS   0.000   0.000   HIS A 517 
 PHE   0.013   0.001   PHE A 390 
 TYR   0.015   0.001   TYR A 506 
 ARG   0.003   0.000   ARG H  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02901 (   60)
  hydrogen bonds       : angle       5.77613 (  141)
  SS BOND              : bond        0.00411 (    6)
  SS BOND              : angle       2.00564 (   12)
  covalent geometry    : bond        0.00297 ( 3301)
  covalent geometry    : angle       0.64498 ( 4487)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 ASP cc_start: 0.7573 (p0) cc_final: 0.7097 (p0)
REVERT: A  466 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7138 (pp)
REVERT: H   22 CYS cc_start: 0.6883 (t) cc_final: 0.6630 (t)
REVERT: H   92 MET cc_start: 0.7814 (ttm) cc_final: 0.7531 (ttm)
REVERT: L   37 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6719 (p90)
REVERT: L   50 TYR cc_start: 0.8049 (p90) cc_final: 0.7805 (p90)
  outliers start: 21
  outliers final: 17
  residues processed: 86
  average time/residue: 0.1135
  time to fit residues: 12.3969
Evaluate side-chains
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0270
   chunk 28 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0270
   chunk 27 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.3496

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.177198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.151975 restraints weight = 4368.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.154037 restraints weight = 3472.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.155632 restraints weight = 2979.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3307  Z= 0.109
  Angle     :  0.657  11.219   4499  Z= 0.322
  Chirality :  0.042   0.121    478
  Planarity :  0.004   0.031    586
  Dihedral  :  4.596  23.563    463
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 31.59 %
    Favored  : 63.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.14 (0.40), residues: 409
  helix: -3.73 (0.89), residues: 15
  sheet: -0.74 (0.49), residues: 125
  loop : -1.69 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP H  47 
 HIS   0.001   0.000   HIS A 503 
 PHE   0.007   0.001   PHE L  99 
 TYR   0.009   0.001   TYR A 506 
 ARG   0.003   0.000   ARG H  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02738 (   60)
  hydrogen bonds       : angle       5.64036 (  141)
  SS BOND              : bond        0.00388 (    6)
  SS BOND              : angle       2.05053 (   12)
  covalent geometry    : bond        0.00263 ( 3301)
  covalent geometry    : angle       0.64941 ( 4487)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  466 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7088 (pp)
REVERT: H   22 CYS cc_start: 0.6806 (t) cc_final: 0.6529 (t)
REVERT: H   92 MET cc_start: 0.7813 (ttm) cc_final: 0.7555 (ttm)
REVERT: L   37 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6685 (p90)
REVERT: L   50 TYR cc_start: 0.7979 (p90) cc_final: 0.7708 (p90)
  outliers start: 18
  outliers final: 16
  residues processed: 82
  average time/residue: 0.1193
  time to fit residues: 12.4277
Evaluate side-chains
  87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  387 ASP
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 TRP
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  467 SER
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   95 CYS
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   37 TYR
Chi-restraints excluded: chain L residue   55 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0060
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 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 = 0.3968 r_free = 0.3968 target = 0.171244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.143787 restraints weight = 4428.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.146382 restraints weight = 3384.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.148267 restraints weight = 2826.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3307  Z= 0.144
  Angle     :  0.674  11.125   4499  Z= 0.333
  Chirality :  0.043   0.122    478
  Planarity :  0.004   0.031    586
  Dihedral  :  4.785  28.693    463
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 31.59 %
    Favored  : 62.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.18 (0.40), residues: 409
  helix: -3.78 (0.87), residues: 15
  sheet: -0.80 (0.49), residues: 126
  loop : -1.70 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP H  47 
 HIS   0.002   0.001   HIS A 503 
 PHE   0.013   0.001   PHE A 390 
 TYR   0.010   0.001   TYR A 506 
 ARG   0.003   0.000   ARG H  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03040 (   60)
  hydrogen bonds       : angle       5.72541 (  141)
  SS BOND              : bond        0.00448 (    6)
  SS BOND              : angle       2.03022 (   12)
  covalent geometry    : bond        0.00348 ( 3301)
  covalent geometry    : angle       0.66675 ( 4487)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1537.54 seconds
wall clock time: 27 minutes 12.79 seconds (1632.79 seconds total)