Starting phenix.real_space_refine
on Tue Mar  3 11:47:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ru4_24696/03_2026/7ru4_24696.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ru4_24696/03_2026/7ru4_24696.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ru4_24696/03_2026/7ru4_24696.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ru4_24696/03_2026/7ru4_24696.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ru4_24696/03_2026/7ru4_24696.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ru4_24696/03_2026/7ru4_24696.map"
  }
  resolution = 3.3
  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=   0.016
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      14      5.16       5
     C    2151      2.51       5
     N     564      2.21       5
     O     653      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3382
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 894
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 894
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 826
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 1610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1610
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 12, 'TRANS': 189}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.77, per 1000 atoms: 0.23
  Number of scatterers: 3382
  At special positions: 0
  Unit cell: (64.89, 99.91, 84.46, 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      14     16.00
     O     653      8.00
     N     564      7.00
     C    2151      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    BETA1-6
      " NAG B   1 " - " FUC B   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A1301 " - " ASN A 331 "
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 113.0 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 9 sheets defined
      15.0% alpha, 36.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 73 through 75
      No H-bonds generated for 'chain 'H' and resid 73 through 75'
    Processing helix  chain 'L' and resid 29 through 31
      No H-bonds generated for 'chain 'L' and resid 29 through 31'
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.799A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.899A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.233A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
      removed outlier: 4.886A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.208A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 11
      removed outlier: 4.048A  pdb=" N   ALA H   9 " --> pdb=" O   LEU H 108 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   THR H 110 " --> pdb=" O   ALA H   9 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE H  34 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   GLY H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 11
      removed outlier: 4.048A  pdb=" N   ALA H   9 " --> pdb=" O   LEU H 108 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   THR H 110 " --> pdb=" O   ALA H   9 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.482A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.500A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454

    127 hydrogen bonds defined for protein.
    297 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: 0.59

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 949
        1.33 -     1.47: 1110
        1.47 -     1.61: 1385
        1.61 -     1.74: 4
        1.74 -     1.88: 16
  Bond restraints: 3464
  Sorted by residual:
  bond pdb=" CB  ILE A 326 "
       pdb=" CG1 ILE A 326 "
    ideal  model  delta    sigma   weight residual
    1.530  1.679 -0.149 2.00e-02 2.50e+03 5.55e+01
  bond pdb=" CG  GLN L   6 "
       pdb=" CD  GLN L   6 "
    ideal  model  delta    sigma   weight residual
    1.516  1.384  0.132 2.50e-02 1.60e+03 2.79e+01
  bond pdb=" CB  TYR L  87 "
       pdb=" CG  TYR L  87 "
    ideal  model  delta    sigma   weight residual
    1.512  1.397  0.115 2.20e-02 2.07e+03 2.75e+01
  bond pdb=" CB  TYR L  36 "
       pdb=" CG  TYR L  36 "
    ideal  model  delta    sigma   weight residual
    1.512  1.398  0.114 2.20e-02 2.07e+03 2.67e+01
  bond pdb=" CB  ILE A 472 "
       pdb=" CG2 ILE A 472 "
    ideal  model  delta    sigma   weight residual
    1.521  1.363  0.158 3.30e-02 9.18e+02 2.29e+01
  ... (remaining 3459 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 4038
        2.58 -     5.15: 576
        5.15 -     7.73: 72
        7.73 -    10.30: 16
       10.30 -    12.88: 4
  Bond angle restraints: 4706
  Sorted by residual:
  angle pdb=" N   ARG L  61 "
        pdb=" CA  ARG L  61 "
        pdb=" C   ARG L  61 "
      ideal   model   delta    sigma   weight residual
     114.56  101.68   12.88 1.27e+00 6.20e-01 1.03e+02
  angle pdb=" N   ALA A 520 "
        pdb=" CA  ALA A 520 "
        pdb=" C   ALA A 520 "
      ideal   model   delta    sigma   weight residual
     108.13  117.09   -8.96 9.00e-01 1.23e+00 9.91e+01
  angle pdb=" N   LEU H  54 "
        pdb=" CA  LEU H  54 "
        pdb=" C   LEU H  54 "
      ideal   model   delta    sigma   weight residual
     113.97  102.00   11.97 1.28e+00 6.10e-01 8.75e+01
  angle pdb=" N   GLN A 474 "
        pdb=" CA  GLN A 474 "
        pdb=" C   GLN A 474 "
      ideal   model   delta    sigma   weight residual
     110.55  122.38  -11.83 1.35e+00 5.49e-01 7.68e+01
  angle pdb=" N   PHE L  98 "
        pdb=" CA  PHE L  98 "
        pdb=" C   PHE L  98 "
      ideal   model   delta    sigma   weight residual
     113.30  124.82  -11.52 1.34e+00 5.57e-01 7.39e+01
  ... (remaining 4701 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.72: 1998
       14.72 -    29.45: 69
       29.45 -    44.17: 15
       44.17 -    58.90: 13
       58.90 -    73.62: 4
  Dihedral angle restraints: 2099
    sinusoidal: 864
      harmonic: 1235
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.11  -45.11     1      1.00e+01 1.00e-02 2.82e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  92 "
           pdb=" CB  CYS H  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   64.13   28.87     1      1.00e+01 1.00e-02 1.19e+01
  dihedral pdb=" SG  CYS A 391 "
           pdb=" CB  CYS A 525 "
           pdb=" SG  CYS A 525 "
           pdb=" CA  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   23.24   55.76     1      2.00e+01 2.50e-03 1.05e+01
  ... (remaining 2096 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 322
       0.087 -    0.173: 141
       0.173 -    0.260: 46
       0.260 -    0.346: 11
       0.346 -    0.433: 6
  Chirality restraints: 526
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.61    0.21 2.00e-02 2.50e+03 1.08e+02
  chirality pdb=" C1  FUC B   3 "
            pdb=" O6  NAG B   1 "
            pdb=" C2  FUC B   3 "
            pdb=" O5  FUC B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.51    0.11 2.00e-02 2.50e+03 2.98e+01
  chirality pdb=" C2  NAG B   2 "
            pdb=" C1  NAG B   2 "
            pdb=" C3  NAG B   2 "
            pdb=" N2  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.92    0.43 2.00e-01 2.50e+01 4.68e+00
  ... (remaining 523 not shown)

  Planarity restraints: 599
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  47 "   -0.057 2.00e-02 2.50e+03   2.67e-02 1.78e+01
        pdb=" CG  TRP H  47 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  47 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  47 "    0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  47 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  47 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  47 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  47 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  47 "    0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  47 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  32 "   -0.056 2.00e-02 2.50e+03   2.94e-02 1.73e+01
        pdb=" CG  TYR L  32 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  32 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  32 "    0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  32 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  32 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  32 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR L  32 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 478 "    0.018 2.00e-02 2.50e+03   3.49e-02 1.22e+01
        pdb=" C   THR A 478 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   THR A 478 "    0.022 2.00e-02 2.50e+03
        pdb=" N   PRO A 479 "    0.020 2.00e-02 2.50e+03
  ... (remaining 596 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 1243
        2.87 -     3.38: 2954
        3.38 -     3.88: 5675
        3.88 -     4.39: 6717
        4.39 -     4.90: 10862
  Nonbonded interactions: 27451
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 340 "
            pdb=" NZ  LYS A 356 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" N   LEU H  54 "
            pdb=" N   ASP H  55 "
     model   vdw
     2.363 2.560
  nonbonded pdb=" N   ARG L  61 "
            pdb=" N   PHE L  62 "
     model   vdw
     2.377 2.560
  nonbonded pdb=" N   PRO A 426 "
            pdb=" O   PRO A 426 "
     model   vdw
     2.440 2.496
  nonbonded pdb=" N   GLN H  97 "
            pdb=" O   GLN H  97 "
     model   vdw
     2.463 2.496
  ... (remaining 27446 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 individual isotropic
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:             9.710
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.570
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
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      :  0.023   0.158   3474  Z= 1.219
  Angle     :  1.905  12.879   4730  Z= 1.262
  Chirality :  0.113   0.433    526
  Planarity :  0.008   0.035    597
  Dihedral  :  9.651  73.619   1295
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 0.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  1.10 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole:  0.06 (0.40), residues: 420
  helix: -3.40 (0.59), residues: 31
  sheet:  1.34 (0.44), residues: 150
  loop : -0.30 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 328 
 TYR   0.056   0.008   TYR L  32 
 PHE   0.026   0.005   PHE A 374 
 TRP   0.057   0.010   TRP H  47 
 HIS   0.003   0.002   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.02292 ( 3464)
  covalent geometry    : angle       1.89411 ( 4706)
  SS BOND              : bond        0.01315 (    6)
  SS BOND              : angle       3.26586 (   12)
  hydrogen bonds       : bond        0.14257 (  119)
  hydrogen bonds       : angle       8.48461 (  297)
  link_BETA1-4         : bond        0.06427 (    1)
  link_BETA1-4         : angle       5.26680 (    3)
  link_BETA1-6         : bond        0.04801 (    1)
  link_BETA1-6         : angle       3.07094 (    3)
  link_NAG-ASN         : bond        0.08070 (    2)
  link_NAG-ASN         : angle       2.71304 (    6)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.182 
Fit side-chains
REVERT: H   89 VAL cc_start: 0.9153 (t) cc_final: 0.8894 (p)
REVERT: A  332 ILE cc_start: 0.8865 (mt) cc_final: 0.8380 (mt)
REVERT: A  336 CYS cc_start: 0.6290 (m) cc_final: 0.5884 (m)
REVERT: A  360 ASN cc_start: 0.8823 (t0) cc_final: 0.8398 (t0)
REVERT: A  453 TYR cc_start: 0.5598 (m-80) cc_final: 0.5330 (m-80)
REVERT: A  458 LYS cc_start: 0.7751 (pttt) cc_final: 0.7151 (mmtm)
  outliers start: 2
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1024
  time to fit residues: 14.2385
Evaluate side-chains
  75 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
H  97 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 100 GLN
A 501 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.086469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.079522 restraints weight = 9650.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.69
r_work: 0.3286 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   3474  Z= 0.222
  Angle     :  0.804  11.138   4730  Z= 0.422
  Chirality :  0.051   0.209    526
  Planarity :  0.005   0.042    597
  Dihedral  :  5.953  27.597    549
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  :  7.95 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole: -0.25 (0.40), residues: 420
  helix: -1.73 (1.24), residues: 25
  sheet:  0.87 (0.42), residues: 150
  loop : -0.65 (0.38), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 454 
 TYR   0.028   0.002   TYR A 495 
 PHE   0.010   0.002   PHE A 486 
 TRP   0.014   0.002   TRP H  47 
 HIS   0.001   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 3464)
  covalent geometry    : angle       0.78936 ( 4706)
  SS BOND              : bond        0.00832 (    6)
  SS BOND              : angle       1.98119 (   12)
  hydrogen bonds       : bond        0.04783 (  119)
  hydrogen bonds       : angle       6.59359 (  297)
  link_BETA1-4         : bond        0.00065 (    1)
  link_BETA1-4         : angle       2.49555 (    3)
  link_BETA1-6         : bond        0.00130 (    1)
  link_BETA1-6         : angle       1.24481 (    3)
  link_NAG-ASN         : bond        0.00755 (    2)
  link_NAG-ASN         : angle       3.04791 (    6)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.165 
Fit side-chains
REVERT: H    4 LEU cc_start: 0.8248 (mt) cc_final: 0.7974 (mm)
REVERT: H  100 LEU cc_start: 0.9383 (mt) cc_final: 0.9106 (mt)
REVERT: L   21 LEU cc_start: 0.8988 (mm) cc_final: 0.8736 (mp)
REVERT: A  356 LYS cc_start: 0.8847 (tttt) cc_final: 0.8104 (tttt)
REVERT: A  420 ASP cc_start: 0.6873 (m-30) cc_final: 0.6101 (t0)
REVERT: A  458 LYS cc_start: 0.7814 (pttt) cc_final: 0.7080 (mmtt)
REVERT: A  460 ASN cc_start: 0.7049 (m-40) cc_final: 0.6417 (m-40)
  outliers start: 14
  outliers final: 6
  residues processed: 94
  average time/residue: 0.0721
  time to fit residues: 8.1912
Evaluate side-chains
  78 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  402 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    0.1980
   chunk 1 optimal weight:    0.0670
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   chunk 19 optimal weight:    0.3980
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0060
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.2134

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

Flipped N/Q/H residues before XYZ refinement:
H  97 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.088081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.080863 restraints weight = 9577.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.75
r_work: 0.3308 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3474  Z= 0.130
  Angle     :  0.686   8.505   4730  Z= 0.355
  Chirality :  0.048   0.228    526
  Planarity :  0.005   0.049    597
  Dihedral  :  5.494  26.210    549
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 11.23 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole: -0.33 (0.40), residues: 420
  helix: -2.07 (1.09), residues: 25
  sheet:  0.92 (0.42), residues: 150
  loop : -0.76 (0.38), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  66 
 TYR   0.018   0.002   TYR A 453 
 PHE   0.019   0.001   PHE A 497 
 TRP   0.010   0.001   TRP H  98 
 HIS   0.001   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3464)
  covalent geometry    : angle       0.65862 ( 4706)
  SS BOND              : bond        0.00509 (    6)
  SS BOND              : angle       2.01589 (   12)
  hydrogen bonds       : bond        0.03607 (  119)
  hydrogen bonds       : angle       6.05207 (  297)
  link_BETA1-4         : bond        0.00402 (    1)
  link_BETA1-4         : angle       2.34780 (    3)
  link_BETA1-6         : bond        0.00259 (    1)
  link_BETA1-6         : angle       1.13751 (    3)
  link_NAG-ASN         : bond        0.00757 (    2)
  link_NAG-ASN         : angle       4.40132 (    6)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.131 
Fit side-chains
REVERT: L   21 LEU cc_start: 0.8978 (mm) cc_final: 0.8745 (mp)
REVERT: A  328 ARG cc_start: 0.7820 (tpt90) cc_final: 0.4823 (pmt-80)
REVERT: A  420 ASP cc_start: 0.7080 (m-30) cc_final: 0.6329 (t0)
REVERT: A  458 LYS cc_start: 0.7900 (pttt) cc_final: 0.6940 (mmtt)
REVERT: A  460 ASN cc_start: 0.7022 (m-40) cc_final: 0.6382 (m-40)
  outliers start: 15
  outliers final: 9
  residues processed: 91
  average time/residue: 0.0675
  time to fit residues: 7.5041
Evaluate side-chains
  83 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   97 GLN
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  402 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.2980
   chunk 36 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
H 105 GLN
L   6 GLN
L  37 GLN
L 100 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.086850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.079737 restraints weight = 9570.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.71
r_work: 0.3271 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.4100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3474  Z= 0.163
  Angle     :  0.684   9.189   4730  Z= 0.343
  Chirality :  0.047   0.203    526
  Planarity :  0.005   0.050    597
  Dihedral  :  5.329  27.635    549
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 13.97 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole: -0.48 (0.40), residues: 420
  helix: -2.15 (1.05), residues: 26
  sheet:  0.88 (0.41), residues: 152
  loop : -0.93 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 346 
 TYR   0.015   0.002   TYR A 453 
 PHE   0.008   0.001   PHE L  83 
 TRP   0.012   0.001   TRP H  98 
 HIS   0.001   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 3464)
  covalent geometry    : angle       0.65750 ( 4706)
  SS BOND              : bond        0.00544 (    6)
  SS BOND              : angle       2.32551 (   12)
  hydrogen bonds       : bond        0.03423 (  119)
  hydrogen bonds       : angle       5.75735 (  297)
  link_BETA1-4         : bond        0.00308 (    1)
  link_BETA1-4         : angle       1.93397 (    3)
  link_BETA1-6         : bond        0.00144 (    1)
  link_BETA1-6         : angle       1.23027 (    3)
  link_NAG-ASN         : bond        0.00795 (    2)
  link_NAG-ASN         : angle       4.06936 (    6)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: H   85 GLU cc_start: 0.8817 (mp0) cc_final: 0.8595 (mp0)
REVERT: H  110 THR cc_start: 0.8274 (p) cc_final: 0.8037 (p)
REVERT: L   21 LEU cc_start: 0.8943 (mm) cc_final: 0.8711 (mp)
REVERT: A  328 ARG cc_start: 0.7813 (tpt90) cc_final: 0.4824 (pmt-80)
REVERT: A  420 ASP cc_start: 0.7130 (m-30) cc_final: 0.6367 (t0)
REVERT: A  458 LYS cc_start: 0.7830 (pttt) cc_final: 0.6987 (mmpt)
REVERT: A  460 ASN cc_start: 0.7144 (m-40) cc_final: 0.6497 (m-40)
  outliers start: 15
  outliers final: 12
  residues processed: 87
  average time/residue: 0.0647
  time to fit residues: 6.9472
Evaluate side-chains
  86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  503 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
H  64 GLN
L 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.087141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.079951 restraints weight = 9670.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 2.72
r_work: 0.3274 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3474  Z= 0.134
  Angle     :  0.647   8.067   4730  Z= 0.327
  Chirality :  0.047   0.193    526
  Planarity :  0.005   0.045    597
  Dihedral  :  5.258  27.744    549
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 12.88 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole: -0.51 (0.40), residues: 420
  helix: -2.21 (1.01), residues: 26
  sheet:  0.92 (0.41), residues: 152
  loop : -0.99 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 346 
 TYR   0.037   0.002   TYR A 453 
 PHE   0.009   0.001   PHE A 497 
 TRP   0.009   0.001   TRP H  98 
 HIS   0.001   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3464)
  covalent geometry    : angle       0.62561 ( 4706)
  SS BOND              : bond        0.00635 (    6)
  SS BOND              : angle       2.24178 (   12)
  hydrogen bonds       : bond        0.03226 (  119)
  hydrogen bonds       : angle       5.56062 (  297)
  link_BETA1-4         : bond        0.00369 (    1)
  link_BETA1-4         : angle       1.98511 (    3)
  link_BETA1-6         : bond        0.00329 (    1)
  link_BETA1-6         : angle       1.13866 (    3)
  link_NAG-ASN         : bond        0.00862 (    2)
  link_NAG-ASN         : angle       3.19218 (    6)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: H   85 GLU cc_start: 0.8805 (mp0) cc_final: 0.8512 (mp0)
REVERT: H  110 THR cc_start: 0.8205 (p) cc_final: 0.7972 (p)
REVERT: L   21 LEU cc_start: 0.8915 (mm) cc_final: 0.8689 (mp)
REVERT: A  328 ARG cc_start: 0.7856 (tpt90) cc_final: 0.4851 (pmt-80)
REVERT: A  420 ASP cc_start: 0.7157 (m-30) cc_final: 0.6336 (t0)
REVERT: A  458 LYS cc_start: 0.7792 (pttt) cc_final: 0.6869 (mmtt)
REVERT: A  460 ASN cc_start: 0.7238 (m-40) cc_final: 0.6623 (m-40)
  outliers start: 17
  outliers final: 13
  residues processed: 87
  average time/residue: 0.0716
  time to fit residues: 7.5955
Evaluate side-chains
  90 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  427 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    0.3980
   chunk 2 optimal weight:    0.0020
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
H 105 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.087270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.080020 restraints weight = 9649.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.76
r_work: 0.3286 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3474  Z= 0.137
  Angle     :  0.661   9.113   4730  Z= 0.332
  Chirality :  0.048   0.202    526
  Planarity :  0.005   0.043    597
  Dihedral  :  5.167  23.928    549
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 15.89 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole: -0.53 (0.40), residues: 420
  helix: -2.15 (1.02), residues: 26
  sheet:  1.01 (0.41), residues: 152
  loop : -1.09 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 346 
 TYR   0.031   0.002   TYR A 453 
 PHE   0.007   0.001   PHE L  83 
 TRP   0.009   0.001   TRP H  98 
 HIS   0.001   0.000   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3464)
  covalent geometry    : angle       0.63270 ( 4706)
  SS BOND              : bond        0.00619 (    6)
  SS BOND              : angle       2.49787 (   12)
  hydrogen bonds       : bond        0.03177 (  119)
  hydrogen bonds       : angle       5.44035 (  297)
  link_BETA1-4         : bond        0.00341 (    1)
  link_BETA1-4         : angle       2.05049 (    3)
  link_BETA1-6         : bond        0.00304 (    1)
  link_BETA1-6         : angle       1.16500 (    3)
  link_NAG-ASN         : bond        0.01106 (    2)
  link_NAG-ASN         : angle       3.92037 (    6)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: H   85 GLU cc_start: 0.8826 (mp0) cc_final: 0.8514 (mp0)
REVERT: H  110 THR cc_start: 0.8241 (p) cc_final: 0.7992 (p)
REVERT: L   21 LEU cc_start: 0.8902 (mm) cc_final: 0.8671 (mp)
REVERT: L   77 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7116 (tmt170)
REVERT: A  328 ARG cc_start: 0.7900 (tpt90) cc_final: 0.4872 (pmt-80)
REVERT: A  333 THR cc_start: 0.9171 (p) cc_final: 0.8944 (p)
REVERT: A  392 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7316 (m-80)
REVERT: A  420 ASP cc_start: 0.7185 (m-30) cc_final: 0.6348 (t0)
REVERT: A  458 LYS cc_start: 0.7710 (pttt) cc_final: 0.6814 (mmpt)
REVERT: A  460 ASN cc_start: 0.7233 (m-40) cc_final: 0.6608 (m-40)
  outliers start: 16
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0784
  time to fit residues: 8.2621
Evaluate side-chains
  89 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  503 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0870
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.086395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.079090 restraints weight = 9839.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.77
r_work: 0.3268 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.4730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3474  Z= 0.151
  Angle     :  0.664   8.303   4730  Z= 0.338
  Chirality :  0.047   0.157    526
  Planarity :  0.005   0.043    597
  Dihedral  :  5.126  24.509    549
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 15.34 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole: -0.55 (0.40), residues: 420
  helix: -1.97 (1.07), residues: 26
  sheet:  1.11 (0.41), residues: 152
  loop : -1.22 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 346 
 TYR   0.021   0.002   TYR L  49 
 PHE   0.007   0.001   PHE A 497 
 TRP   0.009   0.001   TRP H  98 
 HIS   0.001   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3464)
  covalent geometry    : angle       0.63754 ( 4706)
  SS BOND              : bond        0.00737 (    6)
  SS BOND              : angle       2.63878 (   12)
  hydrogen bonds       : bond        0.03220 (  119)
  hydrogen bonds       : angle       5.38233 (  297)
  link_BETA1-4         : bond        0.00225 (    1)
  link_BETA1-4         : angle       2.21125 (    3)
  link_BETA1-6         : bond        0.00227 (    1)
  link_BETA1-6         : angle       1.29577 (    3)
  link_NAG-ASN         : bond        0.01059 (    2)
  link_NAG-ASN         : angle       3.46360 (    6)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: H  110 THR cc_start: 0.8239 (p) cc_final: 0.7978 (p)
REVERT: L   21 LEU cc_start: 0.8895 (mm) cc_final: 0.8647 (mp)
REVERT: L   77 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7091 (tmt170)
REVERT: A  340 GLU cc_start: 0.8807 (pt0) cc_final: 0.8571 (pt0)
REVERT: A  360 ASN cc_start: 0.9237 (t0) cc_final: 0.8968 (t0)
REVERT: A  389 ASP cc_start: 0.7795 (m-30) cc_final: 0.7579 (m-30)
REVERT: A  392 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7072 (m-80)
REVERT: A  420 ASP cc_start: 0.7186 (m-30) cc_final: 0.6306 (t0)
REVERT: A  458 LYS cc_start: 0.7656 (pttt) cc_final: 0.6747 (mmpt)
REVERT: A  460 ASN cc_start: 0.7239 (m-40) cc_final: 0.6560 (m-40)
  outliers start: 17
  outliers final: 12
  residues processed: 87
  average time/residue: 0.0853
  time to fit residues: 8.8769
Evaluate side-chains
  89 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain H residue   89 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  503 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
H  97 GLN
H 105 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.086094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.078868 restraints weight = 9916.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.78
r_work: 0.3259 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.4883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3474  Z= 0.158
  Angle     :  0.686   9.007   4730  Z= 0.349
  Chirality :  0.047   0.151    526
  Planarity :  0.005   0.042    597
  Dihedral  :  5.116  24.679    549
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 16.71 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole: -0.66 (0.41), residues: 420
  helix: -1.96 (1.10), residues: 26
  sheet:  1.12 (0.42), residues: 152
  loop : -1.37 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 346 
 TYR   0.021   0.002   TYR L  49 
 PHE   0.008   0.001   PHE A 329 
 TRP   0.008   0.001   TRP H 103 
 HIS   0.001   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3464)
  covalent geometry    : angle       0.65938 ( 4706)
  SS BOND              : bond        0.00604 (    6)
  SS BOND              : angle       2.88126 (   12)
  hydrogen bonds       : bond        0.03308 (  119)
  hydrogen bonds       : angle       5.34088 (  297)
  link_BETA1-4         : bond        0.00074 (    1)
  link_BETA1-4         : angle       2.35183 (    3)
  link_BETA1-6         : bond        0.00284 (    1)
  link_BETA1-6         : angle       1.12694 (    3)
  link_NAG-ASN         : bond        0.00493 (    2)
  link_NAG-ASN         : angle       3.21431 (    6)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: H  110 THR cc_start: 0.8250 (p) cc_final: 0.7973 (p)
REVERT: L   21 LEU cc_start: 0.8886 (mm) cc_final: 0.8632 (mp)
REVERT: L   77 ARG cc_start: 0.7707 (mmm-85) cc_final: 0.7113 (tmt170)
REVERT: A  389 ASP cc_start: 0.7828 (m-30) cc_final: 0.7618 (m-30)
REVERT: A  392 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6961 (m-80)
REVERT: A  458 LYS cc_start: 0.7603 (pttt) cc_final: 0.6682 (mmpt)
REVERT: A  465 GLU cc_start: 0.7112 (tt0) cc_final: 0.6424 (tt0)
  outliers start: 16
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0666
  time to fit residues: 6.6238
Evaluate side-chains
  87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   89 VAL
Chi-restraints excluded: chain H residue   97 GLN
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  503 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    0.0170
   chunk 39 optimal weight:    0.0470
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0770
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.3074

-------------------------------------------------------------------------------
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 = 0.3520 r_free = 0.3520 target = 0.088053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.080742 restraints weight = 9925.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.82
r_work: 0.3286 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.5110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3474  Z= 0.123
  Angle     :  0.719  11.371   4730  Z= 0.360
  Chirality :  0.047   0.147    526
  Planarity :  0.005   0.043    597
  Dihedral  :  5.475  32.421    549
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.53 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole: -0.61 (0.41), residues: 420
  helix: -2.15 (1.05), residues: 26
  sheet:  1.19 (0.42), residues: 152
  loop : -1.34 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 346 
 TYR   0.022   0.002   TYR L  49 
 PHE   0.006   0.001   PHE A 497 
 TRP   0.020   0.002   TRP H  98 
 HIS   0.001   0.000   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3464)
  covalent geometry    : angle       0.68705 ( 4706)
  SS BOND              : bond        0.00368 (    6)
  SS BOND              : angle       3.01670 (   12)
  hydrogen bonds       : bond        0.03083 (  119)
  hydrogen bonds       : angle       5.42750 (  297)
  link_BETA1-4         : bond        0.00129 (    1)
  link_BETA1-4         : angle       1.81284 (    3)
  link_BETA1-6         : bond        0.00300 (    1)
  link_BETA1-6         : angle       1.27576 (    3)
  link_NAG-ASN         : bond        0.00681 (    2)
  link_NAG-ASN         : angle       4.08498 (    6)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  110 THR cc_start: 0.8157 (p) cc_final: 0.7895 (p)
REVERT: L   21 LEU cc_start: 0.8869 (mm) cc_final: 0.8617 (mp)
REVERT: L   77 ARG cc_start: 0.7676 (mmm-85) cc_final: 0.7149 (tmt170)
REVERT: A  360 ASN cc_start: 0.9199 (t0) cc_final: 0.8960 (t0)
REVERT: A  392 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6505 (m-80)
REVERT: A  458 LYS cc_start: 0.7625 (pttt) cc_final: 0.6646 (mmpt)
REVERT: A  465 GLU cc_start: 0.7122 (tt0) cc_final: 0.6405 (tt0)
  outliers start: 12
  outliers final: 9
  residues processed: 82
  average time/residue: 0.0751
  time to fit residues: 7.4191
Evaluate side-chains
  86 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0670
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.6320

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

Flipped N/Q/H residues before XYZ refinement:
H  97 GLN
H 105 GLN
A 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.086540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.079304 restraints weight = 9902.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.74
r_work: 0.3259 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.5220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3474  Z= 0.157
  Angle     :  0.732  10.955   4730  Z= 0.368
  Chirality :  0.048   0.143    526
  Planarity :  0.005   0.042    597
  Dihedral  :  5.289  25.935    549
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.63 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole: -0.69 (0.41), residues: 420
  helix: -2.17 (1.04), residues: 26
  sheet:  1.20 (0.43), residues: 152
  loop : -1.46 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 346 
 TYR   0.023   0.002   TYR L  49 
 PHE   0.028   0.001   PHE H  79 
 TRP   0.009   0.001   TRP H 103 
 HIS   0.001   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3464)
  covalent geometry    : angle       0.69275 ( 4706)
  SS BOND              : bond        0.00435 (    6)
  SS BOND              : angle       3.17999 (   12)
  hydrogen bonds       : bond        0.03357 (  119)
  hydrogen bonds       : angle       5.46041 (  297)
  link_BETA1-4         : bond        0.00191 (    1)
  link_BETA1-4         : angle       2.02762 (    3)
  link_BETA1-6         : bond        0.00179 (    1)
  link_BETA1-6         : angle       1.20448 (    3)
  link_NAG-ASN         : bond        0.00983 (    2)
  link_NAG-ASN         : angle       4.75612 (    6)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  110 THR cc_start: 0.8245 (p) cc_final: 0.7967 (p)
REVERT: L   21 LEU cc_start: 0.8868 (mm) cc_final: 0.8601 (mp)
REVERT: L   77 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7183 (tmt170)
REVERT: A  360 ASN cc_start: 0.9184 (t0) cc_final: 0.8938 (t0)
REVERT: A  386 LYS cc_start: 0.4905 (mttt) cc_final: 0.3480 (mtpt)
REVERT: A  458 LYS cc_start: 0.7617 (pttt) cc_final: 0.6673 (mmpt)
REVERT: A  465 GLU cc_start: 0.7134 (tt0) cc_final: 0.6457 (tt0)
  outliers start: 11
  outliers final: 9
  residues processed: 79
  average time/residue: 0.0711
  time to fit residues: 6.7607
Evaluate side-chains
  82 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   97 GLN
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.1980
   chunk 37 optimal weight:    0.7980
   chunk 15 optimal weight:    0.4980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 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 = 0.3480 r_free = 0.3480 target = 0.085981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.078729 restraints weight = 10012.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.71
r_work: 0.3254 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.5315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3474  Z= 0.165
  Angle     :  0.732  10.812   4730  Z= 0.368
  Chirality :  0.048   0.154    526
  Planarity :  0.005   0.042    597
  Dihedral  :  5.249  27.509    549
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.90 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 are not related in a simple way.
  whole: -0.78 (0.41), residues: 420
  helix: -2.28 (1.01), residues: 26
  sheet:  1.13 (0.43), residues: 152
  loop : -1.50 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  24 
 TYR   0.051   0.002   TYR A 453 
 PHE   0.008   0.001   PHE A 486 
 TRP   0.013   0.002   TRP H  98 
 HIS   0.001   0.001   HIS L  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3464)
  covalent geometry    : angle       0.69596 ( 4706)
  SS BOND              : bond        0.00456 (    6)
  SS BOND              : angle       3.02262 (   12)
  hydrogen bonds       : bond        0.03356 (  119)
  hydrogen bonds       : angle       5.50602 (  297)
  link_BETA1-4         : bond        0.00094 (    1)
  link_BETA1-4         : angle       2.00967 (    3)
  link_BETA1-6         : bond        0.00172 (    1)
  link_BETA1-6         : angle       1.22995 (    3)
  link_NAG-ASN         : bond        0.00909 (    2)
  link_NAG-ASN         : angle       4.64475 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1142.01 seconds
wall clock time: 20 minutes 14.82 seconds (1214.82 seconds total)