Starting phenix.real_space_refine
on Fri Aug 22 14:50:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k18_36788/08_2025/8k18_36788.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k18_36788/08_2025/8k18_36788.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k18_36788/08_2025/8k18_36788.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k18_36788/08_2025/8k18_36788.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k18_36788/08_2025/8k18_36788.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k18_36788/08_2025/8k18_36788.cif"
  }
  resolution = 3.68
  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=   0.001 sd=   0.019
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 1444 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    2063      2.51       5
     N     541      2.21       5
     O     626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 3246
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 1505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1505
          Classifications: {'peptide': 188}
          Link IDs: {'PTRANS': 10, 'TRANS': 177}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 931
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 113}
    Chain: "D"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 810
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102}
  Time building chain proxies: 0.87, per 1000 atoms: 0.27
  Number of scatterers: 3246
  At special positions: 0
  Unit cell: (64.66, 64.66, 92.22, 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     626      8.00
     N     541      7.00
     C    2063      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.01
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " 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: 0.19
  Conformation dependent library (CDL) restraints added in 76.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  754

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 9 sheets defined
      12.1% alpha, 31.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'E' and resid 338 through 343
    Processing helix  chain 'E' and resid 349 through 353
      removed outlier: 3.891A  pdb=" N   TRP E 353 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 364 through 368
    Processing helix  chain 'E' and resid 405 through 410
    Processing helix  chain 'E' and resid 416 through 422
    Processing helix  chain 'E' and resid 438 through 443
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 4.042A  pdb=" N   ARG C  31 " --> pdb=" O   ILE C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 90
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.747A  pdb=" N   ILE D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.932A  pdb=" N   GLU E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   SER E 399 " --> pdb=" O   GLU E 354 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LYS E 356 " --> pdb=" O   ALA E 397 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   PHE E 392 " --> pdb=" O   VAL E 524 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   VAL E 524 " --> pdb=" O   PHE E 392 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   CYS E 361 " --> pdb=" O   CYS E 525 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.932A  pdb=" N   GLU E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   SER E 399 " --> pdb=" O   GLU E 354 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LYS E 356 " --> pdb=" O   ALA E 397 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454
      removed outlier: 3.577A  pdb=" N   TYR E 453 " --> pdb=" O   GLN E 493 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.800A  pdb=" N   THR C 113 " --> pdb=" O   TYR C  93 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   TYR C  93 " --> pdb=" O   THR C 113 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   THR C  92 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   MET C  34 " --> pdb=" O   ILE C  50 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   ILE C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 17 through 20
      removed outlier: 3.511A  pdb=" N   LEU C  20 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU C  80 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.701A  pdb=" N   VAL D  19 " --> pdb=" O   ILE D  75 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13
      removed outlier: 3.500A  pdb=" N   GLU D 105 " --> pdb=" O   LEU D  11 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 54
      removed outlier: 6.646A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   TYR D  49 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   LEU D  33 " --> pdb=" O   TYR D  49 " (cutoff:3.500A)

    95 hydrogen bonds defined for protein.
    231 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.42

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 627
        1.32 -     1.45: 880
        1.45 -     1.57: 1799
        1.57 -     1.70: 0
        1.70 -     1.82: 20
  Bond restraints: 3326
  Sorted by residual:
  bond pdb=" N   GLY C  91 "
       pdb=" CA  GLY C  91 "
    ideal  model  delta    sigma   weight residual
    1.444  1.478 -0.034 9.10e-03 1.21e+04 1.38e+01
  bond pdb=" CZ  ARG C  38 "
       pdb=" NH2 ARG C  38 "
    ideal  model  delta    sigma   weight residual
    1.330  1.283  0.047 1.30e-02 5.92e+03 1.30e+01
  bond pdb=" CZ  ARG C  71 "
       pdb=" NH1 ARG C  71 "
    ideal  model  delta    sigma   weight residual
    1.323  1.278  0.045 1.40e-02 5.10e+03 1.02e+01
  bond pdb=" N   VAL E 483 "
       pdb=" CA  VAL E 483 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.039 1.23e-02 6.61e+03 9.87e+00
  bond pdb=" CA  PHE E 515 "
       pdb=" C   PHE E 515 "
    ideal  model  delta    sigma   weight residual
    1.524  1.562 -0.038 1.25e-02 6.40e+03 9.48e+00
  ... (remaining 3321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 3178
        1.84 -     3.68: 1098
        3.68 -     5.53: 200
        5.53 -     7.37: 33
        7.37 -     9.21: 5
  Bond angle restraints: 4514
  Sorted by residual:
  angle pdb=" NE  ARG C  71 "
        pdb=" CZ  ARG C  71 "
        pdb=" NH2 ARG C  71 "
      ideal   model   delta    sigma   weight residual
     119.20  126.52   -7.32 9.00e-01 1.23e+00 6.62e+01
  angle pdb=" CA  GLY C  91 "
        pdb=" C   GLY C  91 "
        pdb=" N   THR C  92 "
      ideal   model   delta    sigma   weight residual
     114.50  122.53   -8.03 1.19e+00 7.06e-01 4.56e+01
  angle pdb=" O   GLY C  91 "
        pdb=" C   GLY C  91 "
        pdb=" N   THR C  92 "
      ideal   model   delta    sigma   weight residual
     123.59  117.81    5.78 8.70e-01 1.32e+00 4.41e+01
  angle pdb=" OE1 GLN D  27 "
        pdb=" CD  GLN D  27 "
        pdb=" NE2 GLN D  27 "
      ideal   model   delta    sigma   weight residual
     122.60  116.03    6.57 1.00e+00 1.00e+00 4.32e+01
  angle pdb=" CA  PHE E 515 "
        pdb=" CB  PHE E 515 "
        pdb=" CG  PHE E 515 "
      ideal   model   delta    sigma   weight residual
     113.80  119.75   -5.95 1.00e+00 1.00e+00 3.54e+01
  ... (remaining 4509 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.82: 1737
       15.82 -    31.64: 152
       31.64 -    47.46: 47
       47.46 -    63.28: 11
       63.28 -    79.10: 4
  Dihedral angle restraints: 1951
    sinusoidal: 761
      harmonic: 1190
  Sorted by residual:
  dihedral pdb=" CD  ARG E 457 "
           pdb=" NE  ARG E 457 "
           pdb=" CZ  ARG E 457 "
           pdb=" NH1 ARG E 457 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   67.40  -67.40     1      1.00e+01 1.00e-02 5.91e+01
  dihedral pdb=" CD  ARG C 103 "
           pdb=" NE  ARG C 103 "
           pdb=" CZ  ARG C 103 "
           pdb=" NH1 ARG C 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -39.95   39.95     1      1.00e+01 1.00e-02 2.24e+01
  dihedral pdb=" CB  CYS E 336 "
           pdb=" SG  CYS E 336 "
           pdb=" SG  CYS E 361 "
           pdb=" CB  CYS E 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.61   37.61     1      1.00e+01 1.00e-02 1.99e+01
  ... (remaining 1948 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 234
       0.059 -    0.117: 159
       0.117 -    0.175: 65
       0.175 -    0.233: 20
       0.233 -    0.291: 4
  Chirality restraints: 482
  Sorted by residual:
  chirality pdb=" CA  THR C  92 "
            pdb=" N   THR C  92 "
            pdb=" C   THR C  92 "
            pdb=" CB  THR C  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.23    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CB  VAL C  29 "
            pdb=" CA  VAL C  29 "
            pdb=" CG1 VAL C  29 "
            pdb=" CG2 VAL C  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" CA  ASP E 427 "
            pdb=" N   ASP E 427 "
            pdb=" C   ASP E 427 "
            pdb=" CB  ASP E 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.94e+00
  ... (remaining 479 not shown)

  Planarity restraints: 586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 109 "   -0.150 2.00e-02 2.50e+03   8.15e-02 1.66e+02
        pdb=" CG  TRP C 109 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 109 "    0.117 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 109 "    0.033 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 109 "    0.025 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 109 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 109 "    0.071 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 109 "   -0.115 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 109 "    0.081 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 109 "   -0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 457 "   -1.003 9.50e-02 1.11e+02   4.50e-01 1.22e+02
        pdb=" NE  ARG E 457 "    0.061 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 457 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 457 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 457 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 449 "    0.110 2.00e-02 2.50e+03   7.74e-02 1.20e+02
        pdb=" CG  TYR E 449 "    0.005 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 449 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 449 "   -0.053 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 449 "   -0.071 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 449 "   -0.063 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 449 "   -0.030 2.00e-02 2.50e+03
        pdb=" OH  TYR E 449 "    0.145 2.00e-02 2.50e+03
  ... (remaining 583 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 9
        2.58 -     3.16: 2495
        3.16 -     3.74: 5033
        3.74 -     4.32: 7191
        4.32 -     4.90: 11493
  Nonbonded interactions: 26221
  Sorted by model distance:
  nonbonded pdb=" CG  ARG E 355 "
            pdb=" OD1 ASP E 398 "
     model   vdw
     1.995 3.440
  nonbonded pdb=" OD1 ASN E 417 "
            pdb=" CE2 TYR C  52 "
     model   vdw
     1.999 3.340
  nonbonded pdb=" OD2 ASP E 420 "
            pdb=" OG  SER C  56 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" CG2 VAL C  24 "
            pdb=" CG2 VAL C  29 "
     model   vdw
     2.424 3.880
  nonbonded pdb=" ND2 ASN E 481 "
            pdb=" CG2 VAL E 483 "
     model   vdw
     2.433 3.540
  ... (remaining 26216 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.870
  Find NCS groups from input model:        0.010
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3435
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      :  0.014   0.047   3330  Z= 0.814
  Angle     :  1.855   9.208   4522  Z= 1.236
  Chirality :  0.089   0.291    482
  Planarity :  0.034   0.450    586
  Dihedral  : 13.981  79.096   1185
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  8.73 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.40), residues: 406
  helix: -4.07 (0.61), residues: 24
  sheet: -1.36 (0.48), residues: 89
  loop : -1.00 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.003   ARG C  31 
 TYR   0.145   0.026   TYR E 449 
 PHE   0.069   0.014   PHE E 497 
 TRP   0.150   0.027   TRP C 109 
 HIS   0.025   0.008   HIS D  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.01403 ( 3326)
  covalent geometry    : angle       1.85463 ( 4514)
  SS BOND              : bond        0.01694 (    4)
  SS BOND              : angle       2.10352 (    8)
  hydrogen bonds       : bond        0.26754 (   92)
  hydrogen bonds       : angle      11.25427 (  231)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 33
  average time/residue: 0.1159
  time to fit residues: 4.3635
Evaluate side-chains
  13 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 12
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  457 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:   40.0000
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:   30.0000
   chunk 30 optimal weight:   50.0000
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 106 GLN
** D  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  53 ASN
** D  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.039036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.027656 restraints weight = 45130.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.027946 restraints weight = 45319.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.027989 restraints weight = 43550.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.027989 restraints weight = 42307.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.027989 restraints weight = 42307.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   3330  Z= 0.234
  Angle     :  0.735   8.833   4522  Z= 0.392
  Chirality :  0.047   0.271    482
  Planarity :  0.006   0.046    586
  Dihedral  :  5.962  42.512    459
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 20.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 11.83 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.41), residues: 406
  helix: -3.35 (1.09), residues: 12
  sheet: -1.51 (0.43), residues: 113
  loop : -0.54 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 454 
 TYR   0.016   0.002   TYR E 365 
 PHE   0.015   0.002   PHE E 342 
 TRP   0.013   0.003   TRP D  35 
 HIS   0.003   0.001   HIS D  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 3326)
  covalent geometry    : angle       0.73422 ( 4514)
  SS BOND              : bond        0.00751 (    4)
  SS BOND              : angle       0.98121 (    8)
  hydrogen bonds       : bond        0.04076 (   92)
  hydrogen bonds       : angle       8.20602 (  231)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 14
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  449 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7398 (m-80)
  outliers start: 10
  outliers final: 6
  residues processed: 23
  average time/residue: 0.1314
  time to fit residues: 3.5074
Evaluate side-chains
  19 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 12
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  440 LYS
Chi-restraints excluded: chain E residue  449 TYR
Chi-restraints excluded: chain E residue  457 ARG
Chi-restraints excluded: chain D residue   70 HIS
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  106 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 24 optimal weight:   40.0000
   chunk 18 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN
** D  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.037017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.031582 restraints weight = 46100.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.031282 restraints weight = 146743.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.031251 restraints weight = 150858.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.031227 restraints weight = 126920.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.031193 restraints weight = 118250.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.5803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3330  Z= 0.204
  Angle     :  0.700   9.205   4522  Z= 0.368
  Chirality :  0.044   0.190    482
  Planarity :  0.006   0.043    586
  Dihedral  :  5.767  31.760    459
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 24.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.21 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.41), residues: 406
  helix: -3.03 (1.16), residues: 12
  sheet: -1.44 (0.44), residues: 115
  loop : -0.63 (0.38), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  18 
 TYR   0.016   0.002   TYR E 473 
 PHE   0.028   0.002   PHE E 392 
 TRP   0.013   0.002   TRP D  35 
 HIS   0.002   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 3326)
  covalent geometry    : angle       0.69985 ( 4514)
  SS BOND              : bond        0.00694 (    4)
  SS BOND              : angle       0.89215 (    8)
  hydrogen bonds       : bond        0.03876 (   92)
  hydrogen bonds       : angle       7.76542 (  231)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 14
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  449 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.8009 (m-80)
REVERT: D    4 MET cc_start: 0.3892 (OUTLIER) cc_final: 0.3657 (ttp)
  outliers start: 9
  outliers final: 5
  residues processed: 21
  average time/residue: 0.1008
  time to fit residues: 2.5138
Evaluate side-chains
  19 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 12
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  440 LYS
Chi-restraints excluded: chain E residue  449 TYR
Chi-restraints excluded: chain C residue    3 GLN
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain D residue    4 MET
Chi-restraints excluded: chain D residue   70 HIS
Chi-restraints excluded: chain D residue   72 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 35 optimal weight:   50.0000
   chunk 25 optimal weight:    7.9990
   chunk 20 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  94 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 = 0.3780 r_free = 0.3780 target = 0.037028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.029155 restraints weight = 44991.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.026566 restraints weight = 113467.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.026027 restraints weight = 159465.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.025671 restraints weight = 147491.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.025755 restraints weight = 134490.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.6299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3330  Z= 0.162
  Angle     :  0.644   8.258   4522  Z= 0.335
  Chirality :  0.044   0.184    482
  Planarity :  0.005   0.030    586
  Dihedral  :  5.164  18.506    455
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 21.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.46 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.42), residues: 406
  helix: -2.44 (1.33), residues: 12
  sheet: -1.32 (0.46), residues: 115
  loop : -0.55 (0.39), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  38 
 TYR   0.014   0.002   TYR C  79 
 PHE   0.018   0.002   PHE E 392 
 TRP   0.010   0.001   TRP D  35 
 HIS   0.002   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3326)
  covalent geometry    : angle       0.64346 ( 4514)
  SS BOND              : bond        0.00434 (    4)
  SS BOND              : angle       0.67469 (    8)
  hydrogen bonds       : bond        0.03249 (   92)
  hydrogen bonds       : angle       7.24409 (  231)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 10
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.6169 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 17
  average time/residue: 0.1150
  time to fit residues: 2.3610
Evaluate side-chains
  16 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  440 LYS
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain D residue   70 HIS
Chi-restraints excluded: chain D residue   72 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 2 optimal weight:    0.4980
   chunk 4 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:   50.0000
   chunk 30 optimal weight:   30.0000
   chunk 27 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    5.6988

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

Flipped N/Q/H residues before XYZ refinement:
** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   3 GLN
** D  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.036504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.029663 restraints weight = 45910.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.026762 restraints weight = 108489.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.026378 restraints weight = 157030.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.025921 restraints weight = 187826.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.025894 restraints weight = 159591.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.7203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3330  Z= 0.170
  Angle     :  0.656   9.428   4522  Z= 0.345
  Chirality :  0.044   0.184    482
  Planarity :  0.005   0.033    586
  Dihedral  :  5.157  17.669    455
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 22.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.75 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.42), residues: 406
  helix: -2.96 (0.90), residues: 24
  sheet: -1.28 (0.47), residues: 115
  loop : -0.48 (0.41), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  38 
 TYR   0.019   0.002   TYR E 501 
 PHE   0.017   0.002   PHE E 392 
 TRP   0.011   0.002   TRP D  35 
 HIS   0.003   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3326)
  covalent geometry    : angle       0.65586 ( 4514)
  SS BOND              : bond        0.00293 (    4)
  SS BOND              : angle       0.86723 (    8)
  hydrogen bonds       : bond        0.03261 (   92)
  hydrogen bonds       : angle       6.95783 (  231)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 11
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.6087 (m-80)
REVERT: D    4 MET cc_start: 0.5361 (ttt) cc_final: 0.3710 (tpp)
  outliers start: 12
  outliers final: 6
  residues processed: 23
  average time/residue: 0.0758
  time to fit residues: 2.2204
Evaluate side-chains
  18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 11
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  440 LYS
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   70 HIS
Chi-restraints excluded: chain D residue   72 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 37 optimal weight:   40.0000
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:   30.0000
   chunk 17 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:   40.0000
   chunk 21 optimal weight:   50.0000
   chunk 5 optimal weight:    0.7980
   chunk 10 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   3 GLN
** D  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.036505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.028576 restraints weight = 44436.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.026970 restraints weight = 117609.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.026821 restraints weight = 146915.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.025983 restraints weight = 138663.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.025840 restraints weight = 157281.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.7170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3330  Z= 0.119
  Angle     :  0.599   9.451   4522  Z= 0.319
  Chirality :  0.044   0.163    482
  Planarity :  0.004   0.029    586
  Dihedral  :  4.883  17.853    455
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 18.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.87 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.43), residues: 406
  helix: -2.09 (1.27), residues: 18
  sheet: -1.49 (0.46), residues: 118
  loop : -0.27 (0.41), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  38 
 TYR   0.013   0.001   TYR E 501 
 PHE   0.022   0.001   PHE E 392 
 TRP   0.011   0.001   TRP D  35 
 HIS   0.003   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 3326)
  covalent geometry    : angle       0.59892 ( 4514)
  SS BOND              : bond        0.00272 (    4)
  SS BOND              : angle       0.49372 (    8)
  hydrogen bonds       : bond        0.02903 (   92)
  hydrogen bonds       : angle       6.72385 (  231)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 11
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6164 (m-80)
REVERT: D    4 MET cc_start: 0.5494 (ttt) cc_final: 0.3744 (tpt)
  outliers start: 9
  outliers final: 5
  residues processed: 20
  average time/residue: 0.0990
  time to fit residues: 2.3863
Evaluate side-chains
  17 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 11
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  440 LYS
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain D residue   70 HIS
Chi-restraints excluded: chain D residue   72 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 38 optimal weight:   50.0000
   chunk 20 optimal weight:   20.0000
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   chunk 18 optimal weight:   50.0000
   chunk 32 optimal weight:    9.9990
   chunk 8 optimal weight:   20.0000
   chunk 7 optimal weight:    6.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  30 ASN ** 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 = 0.3764 r_free = 0.3764 target = 0.036112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.029253 restraints weight = 47264.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.026284 restraints weight = 90308.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.025800 restraints weight = 127041.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.025248 restraints weight = 174981.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.025125 restraints weight = 165819.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.7663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3330  Z= 0.161
  Angle     :  0.640   9.171   4522  Z= 0.335
  Chirality :  0.044   0.159    482
  Planarity :  0.004   0.029    586
  Dihedral  :  4.996  18.345    455
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 24.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.00 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.43), residues: 406
  helix: -2.44 (1.06), residues: 24
  sheet: -1.50 (0.46), residues: 117
  loop : -0.21 (0.41), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  38 
 TYR   0.012   0.002   TYR C  79 
 PHE   0.024   0.002   PHE E 392 
 TRP   0.014   0.002   TRP D  35 
 HIS   0.002   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 3326)
  covalent geometry    : angle       0.63937 ( 4514)
  SS BOND              : bond        0.00463 (    4)
  SS BOND              : angle       0.79136 (    8)
  hydrogen bonds       : bond        0.03136 (   92)
  hydrogen bonds       : angle       6.67227 (  231)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 11
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.6283 (m-80)
REVERT: D    4 MET cc_start: 0.6372 (ttt) cc_final: 0.4595 (tpt)
  outliers start: 9
  outliers final: 6
  residues processed: 20
  average time/residue: 0.1036
  time to fit residues: 2.5556
Evaluate side-chains
  18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 11
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  440 LYS
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   70 HIS
Chi-restraints excluded: chain D residue   72 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0070
   chunk 29 optimal weight:    4.9990
   chunk 14 optimal weight:   30.0000
   chunk 15 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0010
   chunk 27 optimal weight:   50.0000
   chunk 5 optimal weight:    0.0020
   chunk 11 optimal weight:   30.0000
   chunk 21 optimal weight:   40.0000
   chunk 17 optimal weight:    5.9990
   overall best weight:    2.2016

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

Flipped N/Q/H residues before XYZ refinement:
** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  30 ASN ** 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 = 0.3777 r_free = 0.3777 target = 0.036344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.029090 restraints weight = 46686.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.026643 restraints weight = 95853.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.025862 restraints weight = 122388.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.025744 restraints weight = 142728.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.025575 restraints weight = 133287.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.7549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3330  Z= 0.109
  Angle     :  0.623  11.707   4522  Z= 0.319
  Chirality :  0.045   0.168    482
  Planarity :  0.004   0.031    586
  Dihedral  :  4.700  17.499    455
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 19.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.72 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.44), residues: 406
  helix: -2.31 (1.22), residues: 18
  sheet: -1.46 (0.46), residues: 118
  loop : -0.14 (0.42), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  38 
 TYR   0.011   0.001   TYR E 473 
 PHE   0.017   0.001   PHE E 392 
 TRP   0.010   0.001   TRP D  35 
 HIS   0.003   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 3326)
  covalent geometry    : angle       0.62328 ( 4514)
  SS BOND              : bond        0.00207 (    4)
  SS BOND              : angle       0.44299 (    8)
  hydrogen bonds       : bond        0.02623 (   92)
  hydrogen bonds       : angle       6.49878 (  231)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 10
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.6232 (m-80)
REVERT: D    4 MET cc_start: 0.5974 (ttt) cc_final: 0.4444 (tpt)
  outliers start: 8
  outliers final: 5
  residues processed: 18
  average time/residue: 0.1029
  time to fit residues: 2.2414
Evaluate side-chains
  16 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  440 LYS
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain D residue   70 HIS
Chi-restraints excluded: chain D residue   72 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 7 optimal weight:   30.0000
   chunk 0 optimal weight:    6.9990
   chunk 12 optimal weight:   40.0000
   chunk 22 optimal weight:   30.0000
   chunk 10 optimal weight:   20.0000
   chunk 21 optimal weight:    9.9990
   chunk 32 optimal weight:   50.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  30 ASN ** 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 = 0.3752 r_free = 0.3752 target = 0.035810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.028977 restraints weight = 47614.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.027880 restraints weight = 104958.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.024801 restraints weight = 129202.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.023619 restraints weight = 197946.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.023678 restraints weight = 235823.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.8462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3330  Z= 0.185
  Angle     :  0.695  10.292   4522  Z= 0.358
  Chirality :  0.045   0.176    482
  Planarity :  0.005   0.031    586
  Dihedral  :  5.095  18.782    455
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 28.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.44 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.44), residues: 406
  helix: -2.42 (1.10), residues: 24
  sheet: -1.62 (0.45), residues: 116
  loop : -0.21 (0.42), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 454 
 TYR   0.016   0.002   TYR E 501 
 PHE   0.026   0.002   PHE E 392 
 TRP   0.017   0.002   TRP D  35 
 HIS   0.003   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 3326)
  covalent geometry    : angle       0.69478 ( 4514)
  SS BOND              : bond        0.00516 (    4)
  SS BOND              : angle       0.84403 (    8)
  hydrogen bonds       : bond        0.03496 (   92)
  hydrogen bonds       : angle       6.79589 (  231)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 12
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6386 (m-80)
REVERT: D    4 MET cc_start: 0.7516 (ttt) cc_final: 0.6684 (tpt)
REVERT: D   18 ARG cc_start: 0.7201 (tpp80) cc_final: 0.6639 (mmm160)
  outliers start: 7
  outliers final: 6
  residues processed: 19
  average time/residue: 0.0975
  time to fit residues: 2.2894
Evaluate side-chains
  19 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 12
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  440 LYS
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain D residue   70 HIS
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   88 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 35 optimal weight:   40.0000
   chunk 16 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 8 optimal weight:   30.0000
   chunk 21 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 1 optimal weight:    0.0070
   chunk 9 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   overall best weight:    4.8006

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

Flipped N/Q/H residues before XYZ refinement:
** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  30 ASN ** 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 = 0.3760 r_free = 0.3760 target = 0.035397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.028537 restraints weight = 47250.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.024750 restraints weight = 110868.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.024710 restraints weight = 147677.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.024379 restraints weight = 176513.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.024382 restraints weight = 144134.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.8559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3330  Z= 0.146
  Angle     :  0.659  10.478   4522  Z= 0.340
  Chirality :  0.044   0.185    482
  Planarity :  0.004   0.031    586
  Dihedral  :  4.902  17.660    455
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 23.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.15 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.44), residues: 406
  helix: -2.49 (1.06), residues: 24
  sheet: -1.59 (0.45), residues: 116
  loop : -0.26 (0.42), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 454 
 TYR   0.014   0.002   TYR E 473 
 PHE   0.020   0.002   PHE E 392 
 TRP   0.013   0.002   TRP D  35 
 HIS   0.003   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3326)
  covalent geometry    : angle       0.65953 ( 4514)
  SS BOND              : bond        0.00363 (    4)
  SS BOND              : angle       0.58877 (    8)
  hydrogen bonds       : bond        0.02987 (   92)
  hydrogen bonds       : angle       6.75087 (  231)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 11
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  347 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6083 (m-80)
REVERT: D    4 MET cc_start: 0.6875 (ttt) cc_final: 0.5721 (tpt)
  outliers start: 9
  outliers final: 8
  residues processed: 20
  average time/residue: 0.0767
  time to fit residues: 1.8722
Evaluate side-chains
  19 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 10
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  335 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  440 LYS
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   70 HIS
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   85 THR
Chi-restraints excluded: chain D residue   88 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 35 optimal weight:   20.0000
   chunk 26 optimal weight:   30.0000
   chunk 29 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   overall best weight:    3.7584

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

Flipped N/Q/H residues before XYZ refinement:
** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  30 ASN ** 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 = 0.3740 r_free = 0.3740 target = 0.034907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 108)---------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.025280 restraints weight = 47895.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.024458 restraints weight = 79440.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.024458 restraints weight = 89074.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.024458 restraints weight = 89075.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.024458 restraints weight = 89075.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.8658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3330  Z= 0.131
  Angle     :  0.637  10.262   4522  Z= 0.327
  Chirality :  0.044   0.190    482
  Planarity :  0.004   0.032    586
  Dihedral  :  4.785  17.539    455
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 22.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.59 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.29 (0.44), residues: 406
  helix: -2.34 (1.10), residues: 24
  sheet: -1.54 (0.45), residues: 116
  loop : -0.29 (0.42), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  38 
 TYR   0.014   0.002   TYR E 473 
 PHE   0.019   0.001   PHE E 392 
 TRP   0.012   0.001   TRP D  35 
 HIS   0.003   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3326)
  covalent geometry    : angle       0.63727 ( 4514)
  SS BOND              : bond        0.00339 (    4)
  SS BOND              : angle       0.49748 (    8)
  hydrogen bonds       : bond        0.02857 (   92)
  hydrogen bonds       : angle       6.57402 (  231)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 775.24 seconds
wall clock time: 14 minutes 1.41 seconds (841.41 seconds total)