Starting phenix.real_space_refine
on Fri Aug 22 13:21:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qtd_18649/08_2025/8qtd_18649.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qtd_18649/08_2025/8qtd_18649.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qtd_18649/08_2025/8qtd_18649.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qtd_18649/08_2025/8qtd_18649.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qtd_18649/08_2025/8qtd_18649.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qtd_18649/08_2025/8qtd_18649.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
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    2058      2.51       5
     N     541      2.21       5
     O     604      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3219
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1566
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 13, 'TRANS': 181}
    Chain: "H"
      Number of atoms: 1021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1021
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
    Chain: "L"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 632
          Classifications: {'peptide': 88}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 83}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 0.99, per 1000 atoms: 0.31
  Number of scatterers: 3219
  At special positions: 0
  Unit cell: (70.8391, 58.424, 97.8602, 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     604      8.00
     N     541      7.00
     C    2058      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 388 " - pdb=" SG  CYS A 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 477 " - pdb=" SG  CYS A 484 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " 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
  Time building additional restraints: 0.16
  Conformation dependent library (CDL) restraints added in 103.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  746

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 10 sheets defined
      13.1% alpha, 37.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 334 through 339
      removed outlier: 4.331A  pdb=" N   VAL A 338 " --> pdb=" O   PRO A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 363
      No H-bonds generated for 'chain 'A' and resid 361 through 363'
    Processing helix  chain 'A' and resid 364 through 369
      removed outlier: 3.896A  pdb=" N   ALA A 369 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 387
      removed outlier: 4.951A  pdb=" N   ASN A 385 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU A 387 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
      removed outlier: 3.854A  pdb=" N   SER A 405 " --> pdb=" O   ASN A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 419
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.785A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 105 through 110
      removed outlier: 3.802A  pdb=" N   GLY H 108 " --> pdb=" O   ASP H 105 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   TYR H 109 " --> pdb=" O   SER H 106 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TYR H 110 " --> pdb=" O   ALA H 107 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 105 through 110'
    Processing helix  chain 'L' and resid 81 through 85
    Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355
    Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 359
      removed outlier: 7.322A  pdb=" N   CYS A 358 " --> pdb=" O   CYS A 521 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 449 through 451
    Processing sheet with id=AA4, first strand: chain 'A' and resid 470 through 471
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.827A  pdb=" N   SER H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP H  73 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.381A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 128 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   SER H  33 " --> pdb=" O   VAL H  99 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.381A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 128 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 121 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   TRP H 121 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 119 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.452A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 107 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.452A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 107 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   VAL L  99 " --> pdb=" O   SER L  92 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR L  94 " --> pdb=" O   VAL L  97 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 18 through 23

    108 hydrogen bonds defined for protein.
    237 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: 0.47

  Time building geometry restraints manager: 0.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1016
        1.34 -     1.46: 888
        1.46 -     1.58: 1386
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 3310
  Sorted by residual:
  bond pdb=" C   GLY L  12 "
       pdb=" N   SER L  13 "
    ideal  model  delta    sigma   weight residual
    1.330  1.348 -0.018 1.47e-02 4.63e+03 1.49e+00
  bond pdb=" N   LYS H  65 "
       pdb=" CA  LYS H  65 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.79e-01
  bond pdb=" C   THR A 412 "
       pdb=" N   GLY A 413 "
    ideal  model  delta    sigma   weight residual
    1.331  1.319  0.011 1.46e-02 4.69e+03 5.78e-01
  bond pdb=" CA  VAL A 379 "
       pdb=" CB  VAL A 379 "
    ideal  model  delta    sigma   weight residual
    1.540  1.550 -0.010 1.36e-02 5.41e+03 4.96e-01
  bond pdb=" CA  LYS A 478 "
       pdb=" CB  LYS A 478 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.011 1.69e-02 3.50e+03 4.57e-01
  ... (remaining 3305 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 4344
        1.10 -     2.20: 112
        2.20 -     3.30: 29
        3.30 -     4.41: 7
        4.41 -     5.51: 2
  Bond angle restraints: 4494
  Sorted by residual:
  angle pdb=" C   GLY L  12 "
        pdb=" N   SER L  13 "
        pdb=" CA  SER L  13 "
      ideal   model   delta    sigma   weight residual
     120.68  124.94   -4.26 1.52e+00 4.33e-01 7.87e+00
  angle pdb=" C   LYS H  65 "
        pdb=" CA  LYS H  65 "
        pdb=" CB  LYS H  65 "
      ideal   model   delta    sigma   weight residual
     110.42  115.55   -5.13 1.99e+00 2.53e-01 6.64e+00
  angle pdb=" N   ASN L  33 "
        pdb=" CA  ASN L  33 "
        pdb=" C   ASN L  33 "
      ideal   model   delta    sigma   weight residual
     114.56  111.40    3.16 1.27e+00 6.20e-01 6.19e+00
  angle pdb=" CA  LYS A 478 "
        pdb=" CB  LYS A 478 "
        pdb=" CG  LYS A 478 "
      ideal   model   delta    sigma   weight residual
     114.10  117.99   -3.89 2.00e+00 2.50e-01 3.79e+00
  angle pdb=" C   CYS A 477 "
        pdb=" N   LYS A 478 "
        pdb=" CA  LYS A 478 "
      ideal   model   delta    sigma   weight residual
     121.54  125.24   -3.70 1.91e+00 2.74e-01 3.76e+00
  ... (remaining 4489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.94: 1750
       11.94 -    23.87: 119
       23.87 -    35.81: 41
       35.81 -    47.74: 6
       47.74 -    59.68: 3
  Dihedral angle restraints: 1919
    sinusoidal: 733
      harmonic: 1186
  Sorted by residual:
  dihedral pdb=" CA  ARG H 112 "
           pdb=" CB  ARG H 112 "
           pdb=" CG  ARG H 112 "
           pdb=" CD  ARG H 112 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  127.06   52.94     3      1.50e+01 4.44e-03 9.16e+00
  dihedral pdb=" N   TYR H 104 "
           pdb=" CA  TYR H 104 "
           pdb=" CB  TYR H 104 "
           pdb=" CG  TYR H 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -112.60   52.60     3      1.50e+01 4.44e-03 9.13e+00
  dihedral pdb=" N   MET H  83 "
           pdb=" CA  MET H  83 "
           pdb=" CB  MET H  83 "
           pdb=" CG  MET H  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -132.62  -47.38     3      1.50e+01 4.44e-03 8.48e+00
  ... (remaining 1916 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 256
       0.027 -    0.053: 137
       0.053 -    0.080: 34
       0.080 -    0.106: 23
       0.106 -    0.133: 18
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CA  ILE A 355 "
            pdb=" N   ILE A 355 "
            pdb=" C   ILE A 355 "
            pdb=" CB  ILE A 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  VAL A 392 "
            pdb=" N   VAL A 392 "
            pdb=" C   VAL A 392 "
            pdb=" CB  VAL A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.79e-01
  chirality pdb=" CA  VAL H  79 "
            pdb=" N   VAL H  79 "
            pdb=" C   VAL H  79 "
            pdb=" CB  VAL H  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  ... (remaining 465 not shown)

  Planarity restraints: 579
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA L  45 "    0.015 5.00e-02 4.00e+02   2.33e-02 8.72e-01
        pdb=" N   PRO L  46 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO L  46 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO L  46 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN H  13 "    0.015 5.00e-02 4.00e+02   2.27e-02 8.22e-01
        pdb=" N   PRO H  14 "   -0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 369 "   -0.014 5.00e-02 4.00e+02   2.10e-02 7.06e-01
        pdb=" N   PRO A 370 "    0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO A 370 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 370 "   -0.012 5.00e-02 4.00e+02
  ... (remaining 576 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 998
        2.82 -     3.34: 2668
        3.34 -     3.86: 5033
        3.86 -     4.38: 6031
        4.38 -     4.90: 10562
  Nonbonded interactions: 25292
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP L  84 "
            pdb=" OH  TYR L  88 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   PHE H  29 "
            pdb=" NH2 ARG H  72 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OD1 ASP A 361 "
            pdb=" OG  SER A 363 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OG  SER A 490 "
            pdb=" O   ARG H 112 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG  SER L  69 "
            pdb=" OG1 THR L  72 "
     model   vdw
     2.378 3.040
  ... (remaining 25287 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:             7.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.840
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
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      :  0.002   0.018   3316  Z= 0.103
  Angle     :  0.488   5.508   4506  Z= 0.265
  Chirality :  0.042   0.133    468
  Planarity :  0.003   0.023    579
  Dihedral  :  9.320  59.680   1155
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  5.56 %
    Favored  : 91.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.44), residues: 403
  helix: -3.83 (0.67), residues: 20
  sheet:  0.62 (0.43), residues: 133
  loop :  0.63 (0.44), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  87 
 TYR   0.008   0.001   TYR H  95 
 PHE   0.004   0.001   PHE H  27 
 TRP   0.005   0.001   TRP A 433 
 HIS   0.001   0.000   HIS H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 ( 3310)
  covalent geometry    : angle       0.48752 ( 4494)
  SS BOND              : bond        0.00164 (    6)
  SS BOND              : angle       0.48717 (   12)
  hydrogen bonds       : bond        0.15611 (  102)
  hydrogen bonds       : angle       6.95054 (  237)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 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: 9
    poor density    : 82
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: H   64 VAL cc_start: 0.7737 (m) cc_final: 0.7352 (m)
REVERT: L   91 SER cc_start: 0.9076 (t) cc_final: 0.8731 (p)
  outliers start: 9
  outliers final: 3
  residues processed: 87
  average time/residue: 0.0890
  time to fit residues: 9.1078
Evaluate side-chains
  62 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0670
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    0.7922

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

Flipped N/Q/H residues before XYZ refinement:
A 471 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.143519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.113887 restraints weight = 5170.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.117427 restraints weight = 3416.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.119963 restraints weight = 2597.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.121702 restraints weight = 2149.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.122825 restraints weight = 1880.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3316  Z= 0.111
  Angle     :  0.483   5.178   4506  Z= 0.250
  Chirality :  0.044   0.126    468
  Planarity :  0.003   0.023    579
  Dihedral  :  5.224  50.620    463
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.70 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.43), residues: 403
  helix: -3.73 (0.73), residues: 19
  sheet:  0.66 (0.44), residues: 126
  loop :  0.49 (0.42), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  67 
 TYR   0.016   0.001   TYR H 109 
 PHE   0.019   0.001   PHE H  68 
 TRP   0.006   0.001   TRP A 433 
 HIS   0.002   0.000   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3310)
  covalent geometry    : angle       0.48280 ( 4494)
  SS BOND              : bond        0.00119 (    6)
  SS BOND              : angle       0.46354 (   12)
  hydrogen bonds       : bond        0.03135 (  102)
  hydrogen bonds       : angle       5.29587 (  237)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   83 MET cc_start: 0.6695 (tpp) cc_final: 0.6399 (tpp)
REVERT: L   91 SER cc_start: 0.9243 (t) cc_final: 0.9008 (p)
  outliers start: 6
  outliers final: 3
  residues processed: 67
  average time/residue: 0.0844
  time to fit residues: 6.7368
Evaluate side-chains
  59 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain H residue  104 TYR
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 33 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.142322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.112812 restraints weight = 5170.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.116044 restraints weight = 3584.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.118433 restraints weight = 2814.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.119623 restraints weight = 2373.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.120856 restraints weight = 2140.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3316  Z= 0.125
  Angle     :  0.503   6.095   4506  Z= 0.251
  Chirality :  0.044   0.132    468
  Planarity :  0.003   0.021    579
  Dihedral  :  5.225  48.906    463
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 12.28 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.43), residues: 403
  helix: -3.60 (0.81), residues: 19
  sheet:  0.54 (0.43), residues: 126
  loop :  0.44 (0.42), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.014   0.001   TYR H  95 
 PHE   0.022   0.001   PHE H  68 
 TRP   0.006   0.001   TRP A 433 
 HIS   0.001   0.000   HIS A 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3310)
  covalent geometry    : angle       0.50351 ( 4494)
  SS BOND              : bond        0.00141 (    6)
  SS BOND              : angle       0.49340 (   12)
  hydrogen bonds       : bond        0.03192 (  102)
  hydrogen bonds       : angle       5.18129 (  237)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: H  109 TYR cc_start: 0.7921 (t80) cc_final: 0.7690 (t80)
REVERT: L   71 ASN cc_start: 0.6388 (m-40) cc_final: 0.5528 (t0)
REVERT: L   91 SER cc_start: 0.9273 (t) cc_final: 0.8961 (p)
  outliers start: 9
  outliers final: 6
  residues processed: 65
  average time/residue: 0.0785
  time to fit residues: 6.1739
Evaluate side-chains
  60 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  119 ASP
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 27 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.141346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.111694 restraints weight = 5174.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.114817 restraints weight = 3594.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.117164 restraints weight = 2850.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.118805 restraints weight = 2404.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.119747 restraints weight = 2126.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3316  Z= 0.132
  Angle     :  0.507   7.221   4506  Z= 0.252
  Chirality :  0.044   0.146    468
  Planarity :  0.003   0.021    579
  Dihedral  :  5.322  51.302    463
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 14.04 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.42), residues: 403
  helix: -3.37 (0.71), residues: 27
  sheet:  0.23 (0.41), residues: 136
  loop :  0.37 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H 112 
 TYR   0.014   0.001   TYR H  95 
 PHE   0.022   0.001   PHE H  68 
 TRP   0.006   0.001   TRP A 433 
 HIS   0.001   0.000   HIS H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3310)
  covalent geometry    : angle       0.50688 ( 4494)
  SS BOND              : bond        0.00139 (    6)
  SS BOND              : angle       0.49400 (   12)
  hydrogen bonds       : bond        0.03119 (  102)
  hydrogen bonds       : angle       5.10686 (  237)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.141 
Fit side-chains
REVERT: H   83 MET cc_start: 0.7194 (tpp) cc_final: 0.6980 (tpp)
REVERT: H  109 TYR cc_start: 0.7861 (t80) cc_final: 0.7585 (t80)
REVERT: L   71 ASN cc_start: 0.6608 (m-40) cc_final: 0.5813 (t0)
REVERT: L   91 SER cc_start: 0.9270 (t) cc_final: 0.8940 (p)
  outliers start: 11
  outliers final: 8
  residues processed: 69
  average time/residue: 0.0908
  time to fit residues: 7.4277
Evaluate side-chains
  67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain H residue   68 PHE
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  119 ASP
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 38 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.139785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.110960 restraints weight = 5150.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.113948 restraints weight = 3567.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.115883 restraints weight = 2816.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.117517 restraints weight = 2407.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.118326 restraints weight = 2144.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3316  Z= 0.143
  Angle     :  0.502   6.115   4506  Z= 0.255
  Chirality :  0.044   0.127    468
  Planarity :  0.003   0.021    579
  Dihedral  :  5.501  55.473    463
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.91 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.42), residues: 403
  helix: -3.44 (0.73), residues: 27
  sheet:  0.13 (0.41), residues: 136
  loop :  0.36 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  67 
 TYR   0.015   0.001   TYR H 114 
 PHE   0.025   0.001   PHE H  68 
 TRP   0.006   0.001   TRP A 433 
 HIS   0.001   0.000   HIS A 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3310)
  covalent geometry    : angle       0.50213 ( 4494)
  SS BOND              : bond        0.00133 (    6)
  SS BOND              : angle       0.47200 (   12)
  hydrogen bonds       : bond        0.03163 (  102)
  hydrogen bonds       : angle       5.11056 (  237)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: H  109 TYR cc_start: 0.7761 (t80) cc_final: 0.7552 (t80)
REVERT: L   71 ASN cc_start: 0.6772 (m-40) cc_final: 0.5971 (t0)
REVERT: L   91 SER cc_start: 0.9281 (t) cc_final: 0.8935 (p)
  outliers start: 9
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0811
  time to fit residues: 6.3851
Evaluate side-chains
  66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain H residue   68 PHE
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  114 TYR
Chi-restraints excluded: chain H residue  119 ASP
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0040
   chunk 20 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.6592

-------------------------------------------------------------------------------
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 = 0.3802 r_free = 0.3802 target = 0.142078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.112892 restraints weight = 5061.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.115974 restraints weight = 3540.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.118244 restraints weight = 2799.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.119824 restraints weight = 2366.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.120379 restraints weight = 2102.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3316  Z= 0.095
  Angle     :  0.479   6.844   4506  Z= 0.239
  Chirality :  0.043   0.126    468
  Planarity :  0.003   0.027    579
  Dihedral  :  5.498  57.086    463
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.96 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.42), residues: 403
  helix: -3.48 (0.70), residues: 27
  sheet:  0.53 (0.42), residues: 126
  loop :  0.34 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.013   0.001   TYR H 114 
 PHE   0.020   0.001   PHE H  68 
 TRP   0.006   0.001   TRP A 433 
 HIS   0.001   0.000   HIS H 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 3310)
  covalent geometry    : angle       0.47907 ( 4494)
  SS BOND              : bond        0.00157 (    6)
  SS BOND              : angle       0.48095 (   12)
  hydrogen bonds       : bond        0.02807 (  102)
  hydrogen bonds       : angle       4.83108 (  237)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: H   80 PHE cc_start: 0.7680 (m-80) cc_final: 0.7435 (m-80)
REVERT: L   71 ASN cc_start: 0.6575 (m-40) cc_final: 0.5898 (t0)
REVERT: L   91 SER cc_start: 0.9276 (t) cc_final: 0.8918 (p)
  outliers start: 8
  outliers final: 7
  residues processed: 69
  average time/residue: 0.0869
  time to fit residues: 7.1361
Evaluate side-chains
  65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain H residue   68 PHE
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  114 TYR
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 2 optimal weight:    0.6980
   chunk 20 optimal weight:    0.1980
   chunk 7 optimal weight:    0.4980
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 = 0.3765 r_free = 0.3765 target = 0.140238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.114022 restraints weight = 5236.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.116518 restraints weight = 3896.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.118196 restraints weight = 3182.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.119251 restraints weight = 2780.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.120339 restraints weight = 2526.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3316  Z= 0.144
  Angle     :  0.512   6.519   4506  Z= 0.260
  Chirality :  0.044   0.127    468
  Planarity :  0.003   0.026    579
  Dihedral  :  5.569  59.322    463
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.54 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.41), residues: 403
  helix: -3.79 (0.64), residues: 27
  sheet:  0.25 (0.42), residues: 129
  loop :  0.26 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.014   0.001   TYR H  95 
 PHE   0.023   0.001   PHE H  68 
 TRP   0.006   0.001   TRP A 433 
 HIS   0.001   0.000   HIS H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3310)
  covalent geometry    : angle       0.51195 ( 4494)
  SS BOND              : bond        0.00113 (    6)
  SS BOND              : angle       0.42733 (   12)
  hydrogen bonds       : bond        0.03143 (  102)
  hydrogen bonds       : angle       5.04796 (  237)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: L   71 ASN cc_start: 0.6770 (m-40) cc_final: 0.6109 (t0)
REVERT: L   91 SER cc_start: 0.9242 (t) cc_final: 0.8890 (p)
  outliers start: 8
  outliers final: 8
  residues processed: 64
  average time/residue: 0.0806
  time to fit residues: 6.2232
Evaluate side-chains
  66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain H residue   68 PHE
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  114 TYR
Chi-restraints excluded: chain H residue  119 ASP
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0020
   overall best weight:    0.7390

-------------------------------------------------------------------------------
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 = 0.3783 r_free = 0.3783 target = 0.141743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.115739 restraints weight = 5197.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.118149 restraints weight = 3855.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.119963 restraints weight = 3152.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.121241 restraints weight = 2726.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.122112 restraints weight = 2454.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3316  Z= 0.103
  Angle     :  0.496   7.300   4506  Z= 0.249
  Chirality :  0.043   0.127    468
  Planarity :  0.003   0.026    579
  Dihedral  :  5.497  57.468    463
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.84 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.42), residues: 403
  helix: -3.83 (0.63), residues: 27
  sheet:  0.36 (0.42), residues: 129
  loop :  0.32 (0.42), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 112 
 TYR   0.013   0.001   TYR H 114 
 PHE   0.019   0.001   PHE H  68 
 TRP   0.006   0.001   TRP A 433 
 HIS   0.001   0.000   HIS A 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 3310)
  covalent geometry    : angle       0.49621 ( 4494)
  SS BOND              : bond        0.00141 (    6)
  SS BOND              : angle       0.42763 (   12)
  hydrogen bonds       : bond        0.02834 (  102)
  hydrogen bonds       : angle       4.89042 (  237)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: H   80 PHE cc_start: 0.7545 (m-80) cc_final: 0.7316 (m-80)
REVERT: L   71 ASN cc_start: 0.6716 (m-40) cc_final: 0.6109 (t0)
REVERT: L   91 SER cc_start: 0.9217 (t) cc_final: 0.8893 (p)
  outliers start: 8
  outliers final: 7
  residues processed: 69
  average time/residue: 0.0880
  time to fit residues: 7.2166
Evaluate side-chains
  66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain H residue   68 PHE
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  114 TYR
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0670
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    1.8126

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.138213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.110729 restraints weight = 5283.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.113579 restraints weight = 3766.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.115374 restraints weight = 2999.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.116972 restraints weight = 2575.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.117586 restraints weight = 2284.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3316  Z= 0.188
  Angle     :  0.556   6.752   4506  Z= 0.286
  Chirality :  0.045   0.135    468
  Planarity :  0.004   0.034    579
  Dihedral  :  5.546  53.456    463
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.37 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.40), residues: 403
  helix: -4.38 (0.41), residues: 28
  sheet:  0.18 (0.42), residues: 127
  loop :  0.06 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.016   0.001   TYR H 114 
 PHE   0.029   0.002   PHE H  68 
 TRP   0.005   0.001   TRP A 433 
 HIS   0.002   0.001   HIS H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 3310)
  covalent geometry    : angle       0.55632 ( 4494)
  SS BOND              : bond        0.00131 (    6)
  SS BOND              : angle       0.45493 (   12)
  hydrogen bonds       : bond        0.03372 (  102)
  hydrogen bonds       : angle       5.31489 (  237)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: L   71 ASN cc_start: 0.6906 (m-40) cc_final: 0.6183 (t0)
REVERT: L   91 SER cc_start: 0.9275 (t) cc_final: 0.8935 (p)
  outliers start: 9
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0760
  time to fit residues: 5.7973
Evaluate side-chains
  66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain H residue   68 PHE
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  114 TYR
Chi-restraints excluded: chain H residue  119 ASP
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.140469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.114315 restraints weight = 5164.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.116794 restraints weight = 3873.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.118300 restraints weight = 3169.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.119706 restraints weight = 2763.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.120415 restraints weight = 2486.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3316  Z= 0.119
  Angle     :  0.519   7.188   4506  Z= 0.264
  Chirality :  0.044   0.129    468
  Planarity :  0.003   0.031    579
  Dihedral  :  5.630  58.664    463
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.54 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.40), residues: 403
  helix: -3.95 (0.61), residues: 27
  sheet:  0.17 (0.43), residues: 118
  loop :  0.18 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 112 
 TYR   0.014   0.001   TYR H 114 
 PHE   0.023   0.001   PHE H  68 
 TRP   0.006   0.001   TRP A 433 
 HIS   0.001   0.000   HIS A 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 3310)
  covalent geometry    : angle       0.51939 ( 4494)
  SS BOND              : bond        0.00128 (    6)
  SS BOND              : angle       0.52539 (   12)
  hydrogen bonds       : bond        0.02991 (  102)
  hydrogen bonds       : angle       5.10314 (  237)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: H  118 MET cc_start: 0.8589 (mtm) cc_final: 0.8359 (mtt)
REVERT: L   71 ASN cc_start: 0.6805 (m-40) cc_final: 0.6233 (t0)
REVERT: L   91 SER cc_start: 0.9264 (t) cc_final: 0.8928 (p)
  outliers start: 9
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0689
  time to fit residues: 5.5964
Evaluate side-chains
  68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain H residue   68 PHE
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  114 TYR
Chi-restraints excluded: chain H residue  119 ASP
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.3754 r_free = 0.3754 target = 0.139494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.113181 restraints weight = 5273.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.115656 restraints weight = 3947.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.117411 restraints weight = 3215.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.118610 restraints weight = 2780.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.119264 restraints weight = 2507.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3316  Z= 0.153
  Angle     :  0.535   7.209   4506  Z= 0.276
  Chirality :  0.044   0.147    468
  Planarity :  0.004   0.037    579
  Dihedral  :  5.637  57.673    463
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.96 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.40), residues: 403
  helix: -4.33 (0.42), residues: 28
  sheet:  0.22 (0.43), residues: 116
  loop :  0.10 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.021   0.001   TYR H 109 
 PHE   0.027   0.001   PHE H  68 
 TRP   0.005   0.001   TRP A 433 
 HIS   0.001   0.000   HIS H 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3310)
  covalent geometry    : angle       0.53524 ( 4494)
  SS BOND              : bond        0.00117 (    6)
  SS BOND              : angle       0.48400 (   12)
  hydrogen bonds       : bond        0.03200 (  102)
  hydrogen bonds       : angle       5.21366 (  237)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 994.11 seconds
wall clock time: 17 minutes 46.80 seconds (1066.80 seconds total)