Starting phenix.real_space_refine
on Fri Aug 22 15:12:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hg7_34737/08_2025/8hg7_34737.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hg7_34737/08_2025/8hg7_34737.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hg7_34737/08_2025/8hg7_34737.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hg7_34737/08_2025/8hg7_34737.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hg7_34737/08_2025/8hg7_34737.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hg7_34737/08_2025/8hg7_34737.map"
  }
  resolution = 3.1
  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=   0.010
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: 6
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     Cl      1      4.86       5
     Na      1      4.78       5
     C    3169      2.51       5
     N     786      2.21       5
     O     813      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  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: 4808
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4532
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 590, 4532
          Classifications: {'peptide': 590}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 562}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 231
          Classifications: {'peptide': 29}
          Link IDs: {'PTRANS': 1, 'TRANS': 27}
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 45
          Unusual residues: {' NA': 1, 'LFL': 1, 'NAG': 1}
          Classifications: {'undetermined': 3, 'water': 2}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.60, per 1000 atoms: 0.33
  Number of scatterers: 4808
  At special positions: 0
  Unit cell: (74.1469, 74.1469, 95.1736, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      38     16.00
     Na      1     11.00
     O     813      8.00
     N     786      7.00
     C    3169      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 255 " - pdb=" SG  CYS A 511 " distance=2.33
    Simple disulfide: pdb=" SG  CYS A 345 " - pdb=" SG  CYS A 351 " distance=2.41
    Simple disulfide: pdb=" SG  CYS A 355 " - pdb=" SG  CYS A 361 " distance=2.30
    Simple disulfide: pdb=" SG  CYS A 517 " - pdb=" SG  CYS A 522 " distance=2.28

  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: 0.39
  Conformation dependent library (CDL) restraints added in 178.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1124

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      82.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 47
    Processing helix  chain 'A' and resid 51 through 58
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 77 through 92
      removed outlier: 3.833A  pdb=" N   PHE A  81 " --> pdb=" O   GLY A  77 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA A  85 " --> pdb=" O   PHE A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 120
      removed outlier: 4.178A  pdb=" N   GLU A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA A 102 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   PHE A 104 " --> pdb=" O   TRP A 100 " (cutoff:3.500A)
      Proline residue:  A 115  - end of helix
    Processing helix  chain 'A' and resid 124 through 134
      removed outlier: 3.606A  pdb=" N   LEU A 129 " --> pdb=" O   MET A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 154
      removed outlier: 3.795A  pdb=" N   LEU A 140 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 170
      removed outlier: 3.634A  pdb=" N   ASP A 158 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 193
      removed outlier: 4.490A  pdb=" N   GLY A 192 " --> pdb=" O   TYR A 188 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLY A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 224
      removed outlier: 3.835A  pdb=" N   VAL A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   PHE A 206 " --> pdb=" O   THR A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 233
      removed outlier: 3.521A  pdb=" N   LEU A 229 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE A 230 " --> pdb=" O   TYR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 3.634A  pdb=" N   TYR A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG A 257 " --> pdb=" O   SER A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 252 through 257'
    Processing helix  chain 'A' and resid 275 through 293
    Processing helix  chain 'A' and resid 294 through 299
    Processing helix  chain 'A' and resid 306 through 321
    Processing helix  chain 'A' and resid 322 through 328
      removed outlier: 3.999A  pdb=" N   PHE A 326 " --> pdb=" O   LEU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 339
    Processing helix  chain 'A' and resid 339 through 344
    Processing helix  chain 'A' and resid 347 through 356
    Processing helix  chain 'A' and resid 361 through 363
      No H-bonds generated for 'chain 'A' and resid 361 through 363'
    Processing helix  chain 'A' and resid 364 through 374
      removed outlier: 3.615A  pdb=" N   MET A 374 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 409
    Processing helix  chain 'A' and resid 409 through 414
    Processing helix  chain 'A' and resid 420 through 446
      removed outlier: 3.592A  pdb=" N   VAL A 430 " --> pdb=" O   GLY A 426 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A 431 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)
      Proline residue:  A 442  - end of helix
    Processing helix  chain 'A' and resid 447 through 449
      No H-bonds generated for 'chain 'A' and resid 447 through 449'
    Processing helix  chain 'A' and resid 450 through 464
      removed outlier: 3.847A  pdb=" N   ASP A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLN A 457 " --> pdb=" O   PHE A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 477
      removed outlier: 3.571A  pdb=" N   LEU A 473 " --> pdb=" O   ALA A 469 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL A 477 " --> pdb=" O   LEU A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 507
      removed outlier: 3.596A  pdb=" N   ARG A 499 " --> pdb=" O   MET A 495 " (cutoff:3.500A)
      Proline residue:  A 502  - end of helix
      removed outlier: 3.983A  pdb=" N   PHE A 506 " --> pdb=" O   PRO A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 523
      removed outlier: 3.577A  pdb=" N   CYS A 522 " --> pdb=" O   PRO A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 548
      removed outlier: 3.672A  pdb=" N   ILE A 531 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 556
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 3.671A  pdb=" N   ARG A 564 " --> pdb=" O   PHE A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 671
      removed outlier: 3.509A  pdb=" N   LEU A 658 " --> pdb=" O   ASN A 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 55

    338 hydrogen bonds defined for protein.
    1005 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: 0.54

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 709
        1.29 -     1.43: 1412
        1.43 -     1.57: 2753
        1.57 -     1.72: 1
        1.72 -     1.86: 59
  Bond restraints: 4934
  Sorted by residual:
  bond pdb=" C   MET A 325 "
       pdb=" O   MET A 325 "
    ideal  model  delta    sigma   weight residual
    1.237  1.147  0.090 1.19e-02 7.06e+03 5.67e+01
  bond pdb=" C   PRO A 502 "
       pdb=" O   PRO A 502 "
    ideal  model  delta    sigma   weight residual
    1.238  1.149  0.089 1.33e-02 5.65e+03 4.50e+01
  bond pdb=" C   PRO A 115 "
       pdb=" O   PRO A 115 "
    ideal  model  delta    sigma   weight residual
    1.235  1.153  0.082 1.30e-02 5.92e+03 3.94e+01
  bond pdb=" C   PRO A 324 "
       pdb=" O   PRO A 324 "
    ideal  model  delta    sigma   weight residual
    1.238  1.162  0.076 1.33e-02 5.65e+03 3.24e+01
  bond pdb=" C   TRP A 100 "
       pdb=" O   TRP A 100 "
    ideal  model  delta    sigma   weight residual
    1.236  1.308 -0.071 1.29e-02 6.01e+03 3.07e+01
  ... (remaining 4929 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 4541
        2.14 -     4.28: 1850
        4.28 -     6.43: 295
        6.43 -     8.57: 37
        8.57 -    10.71: 5
  Bond angle restraints: 6728
  Sorted by residual:
  angle pdb=" N   PHE A 113 "
        pdb=" CA  PHE A 113 "
        pdb=" C   PHE A 113 "
      ideal   model   delta    sigma   weight residual
     113.55  104.63    8.92 1.26e+00 6.30e-01 5.01e+01
  angle pdb=" CA  ASP A 261 "
        pdb=" CB  ASP A 261 "
        pdb=" CG  ASP A 261 "
      ideal   model   delta    sigma   weight residual
     112.60  119.63   -7.03 1.00e+00 1.00e+00 4.95e+01
  angle pdb=" C   PHE A  98 "
        pdb=" CA  PHE A  98 "
        pdb=" CB  PHE A  98 "
      ideal   model   delta    sigma   weight residual
     110.88  121.59  -10.71 1.57e+00 4.06e-01 4.65e+01
  angle pdb=" CA  PHE A 148 "
        pdb=" C   PHE A 148 "
        pdb=" O   PHE A 148 "
      ideal   model   delta    sigma   weight residual
     120.42  113.58    6.84 1.06e+00 8.90e-01 4.16e+01
  angle pdb=" N   CYS A 522 "
        pdb=" CA  CYS A 522 "
        pdb=" C   CYS A 522 "
      ideal   model   delta    sigma   weight residual
     110.97  118.00   -7.03 1.09e+00 8.42e-01 4.16e+01
  ... (remaining 6723 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 2568
       17.40 -    34.80: 241
       34.80 -    52.19: 52
       52.19 -    69.59: 12
       69.59 -    86.99: 3
  Dihedral angle restraints: 2876
    sinusoidal: 1112
      harmonic: 1764
  Sorted by residual:
  dihedral pdb=" CB  CYS A 255 "
           pdb=" SG  CYS A 255 "
           pdb=" SG  CYS A 511 "
           pdb=" CB  CYS A 511 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -21.88  -64.12     1      1.00e+01 1.00e-02 5.41e+01
  dihedral pdb=" C   PRO A 502 "
           pdb=" N   PRO A 502 "
           pdb=" CA  PRO A 502 "
           pdb=" CB  PRO A 502 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -134.66   13.96     0      2.50e+00 1.60e-01 3.12e+01
  dihedral pdb=" CA  GLY A 418 "
           pdb=" C   GLY A 418 "
           pdb=" N   ASP A 419 "
           pdb=" CA  ASP A 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.13  -27.87     0      5.00e+00 4.00e-02 3.11e+01
  ... (remaining 2873 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.132: 664
       0.132 -    0.263: 115
       0.263 -    0.395: 2
       0.395 -    0.526: 0
       0.526 -    0.658: 1
  Chirality restraints: 782
  Sorted by residual:
  chirality pdb=" CA  PRO A 502 "
            pdb=" N   PRO A 502 "
            pdb=" C   PRO A 502 "
            pdb=" CB  PRO A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.06    0.66 2.00e-01 2.50e+01 1.08e+01
  chirality pdb=" CA  PRO A 367 "
            pdb=" N   PRO A 367 "
            pdb=" C   PRO A 367 "
            pdb=" CB  PRO A 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  ILE A 251 "
            pdb=" N   ILE A 251 "
            pdb=" C   ILE A 251 "
            pdb=" CB  ILE A 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.27 2.00e-01 2.50e+01 1.89e+00
  ... (remaining 779 not shown)

  Planarity restraints: 824
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  60 "    0.631 9.50e-02 1.11e+02   2.83e-01 4.89e+01
        pdb=" NE  ARG A  60 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  60 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  60 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  60 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 110 "    0.024 2.00e-02 2.50e+03   4.61e-02 2.12e+01
        pdb=" C   GLY A 110 "   -0.080 2.00e-02 2.50e+03
        pdb=" O   GLY A 110 "    0.029 2.00e-02 2.50e+03
        pdb=" N   TRP A 111 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  98 "   -0.017 2.00e-02 2.50e+03   3.31e-02 1.10e+01
        pdb=" C   PHE A  98 "    0.057 2.00e-02 2.50e+03
        pdb=" O   PHE A  98 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLU A  99 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 821 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 84
        2.68 -     3.23: 4656
        3.23 -     3.79: 7594
        3.79 -     4.34: 10798
        4.34 -     4.90: 17313
  Nonbonded interactions: 40445
  Sorted by model distance:
  nonbonded pdb=" O   ALA A  73 "
            pdb="NA    NA A 803 "
     model   vdw
     2.121 2.470
  nonbonded pdb=" O   ILE A  76 "
            pdb="NA    NA A 803 "
     model   vdw
     2.133 2.470
  nonbonded pdb=" ND2 ASN A 250 "
            pdb=" C1  NAG A 801 "
     model   vdw
     2.200 3.550
  nonbonded pdb=" OH  TYR A 128 "
            pdb=" O   LEU A 559 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   ARG A 259 "
            pdb=" OG  SER A 262 "
     model   vdw
     2.358 3.040
  ... (remaining 40440 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:             0.110
  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:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.650
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
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      :  0.019   0.375   4938  Z= 1.290
  Angle     :  2.197  10.711   6736  Z= 1.613
  Chirality :  0.094   0.658    782
  Planarity :  0.012   0.283    824
  Dihedral  : 14.288  86.989   1740
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  6.36 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.36 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.29), residues: 613
  helix: -1.54 (0.20), residues: 443
  sheet:  None (None), residues: 0
  loop : -1.90 (0.44), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 336 
 TYR   0.030   0.005   TYR A 128 
 PHE   0.022   0.004   PHE A 113 
 TRP   0.022   0.004   TRP A 487 
 HIS   0.008   0.002   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.01667 ( 4934)
  covalent geometry    : angle       2.19153 ( 6728)
  SS BOND              : bond        0.30107 (    4)
  SS BOND              : angle       5.17466 (    8)
  hydrogen bonds       : bond        0.18480 (  338)
  hydrogen bonds       : angle       8.38574 ( 1005)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   99 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8147 (mm-30)
REVERT: A  104 PHE cc_start: 0.7585 (m-80) cc_final: 0.7376 (m-80)
REVERT: A  150 TYR cc_start: 0.8535 (m-10) cc_final: 0.8250 (m-10)
REVERT: A  167 GLN cc_start: 0.8475 (tt0) cc_final: 0.8229 (tt0)
REVERT: A  191 THR cc_start: 0.8067 (m) cc_final: 0.7826 (m)
REVERT: A  216 MET cc_start: 0.8022 (ttp) cc_final: 0.7760 (ttp)
REVERT: A  244 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7198 (mm-30)
REVERT: A  323 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.7955 (p)
REVERT: A  328 MET cc_start: 0.8610 (mtt) cc_final: 0.8222 (mtt)
REVERT: A  382 MET cc_start: 0.8263 (mmm) cc_final: 0.8036 (mmm)
REVERT: A  412 ARG cc_start: 0.6987 (ttt180) cc_final: 0.5933 (ttp80)
REVERT: A  495 MET cc_start: 0.7652 (mtp) cc_final: 0.7261 (mtt)
REVERT: A  500 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7392 (tt)
REVERT: A  641 GLU cc_start: 0.6454 (mm-30) cc_final: 0.5791 (mt-10)
  outliers start: 11
  outliers final: 5
  residues processed: 85
  average time/residue: 0.1177
  time to fit residues: 11.8258
Evaluate side-chains
  76 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 PRO
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  466 PRO
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  560 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0970
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 295 GLN
A 399 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.123665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.103326 restraints weight = 5101.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.27
r_work: 0.2913 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4938  Z= 0.135
  Angle     :  0.637   7.469   6736  Z= 0.333
  Chirality :  0.042   0.196    782
  Planarity :  0.005   0.038    824
  Dihedral  :  6.958  57.949    739
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  8.75 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.34), residues: 613
  helix:  0.91 (0.24), residues: 451
  sheet:  None (None), residues: 0
  loop : -1.18 (0.50), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 267 
 TYR   0.028   0.001   TYR A 256 
 PHE   0.011   0.001   PHE A  98 
 TRP   0.013   0.001   TRP A  42 
 HIS   0.003   0.000   HIS A  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4934)
  covalent geometry    : angle       0.63468 ( 6728)
  SS BOND              : bond        0.00328 (    4)
  SS BOND              : angle       1.71198 (    8)
  hydrogen bonds       : bond        0.04399 (  338)
  hydrogen bonds       : angle       5.54813 ( 1005)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A   91 SER cc_start: 0.8815 (m) cc_final: 0.8472 (p)
REVERT: A  191 THR cc_start: 0.8709 (m) cc_final: 0.8506 (m)
REVERT: A  198 MET cc_start: 0.8037 (mtt) cc_final: 0.7762 (mtt)
REVERT: A  216 MET cc_start: 0.8558 (ttp) cc_final: 0.8179 (ttp)
REVERT: A  299 GLN cc_start: 0.8879 (mt0) cc_final: 0.8648 (tt0)
REVERT: A  323 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8901 (p)
REVERT: A  352 ARG cc_start: 0.7330 (ttm110) cc_final: 0.6963 (ttm170)
REVERT: A  382 MET cc_start: 0.8367 (mmm) cc_final: 0.8098 (mmm)
REVERT: A  412 ARG cc_start: 0.7442 (ttt180) cc_final: 0.6868 (ttp80)
REVERT: A  427 ARG cc_start: 0.8806 (mtt180) cc_final: 0.8590 (mtt90)
REVERT: A  445 GLN cc_start: 0.7563 (mm110) cc_final: 0.7329 (mt0)
REVERT: A  553 ARG cc_start: 0.7762 (mtp-110) cc_final: 0.7312 (ttp80)
REVERT: A  554 LYS cc_start: 0.8104 (pttt) cc_final: 0.7844 (pttm)
  outliers start: 8
  outliers final: 5
  residues processed: 83
  average time/residue: 0.1009
  time to fit residues: 10.0004
Evaluate side-chains
  76 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  642 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 47 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 557 HIS
A 656 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.120803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.100312 restraints weight = 5173.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 1.28
r_work: 0.2872 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4938  Z= 0.138
  Angle     :  0.606   7.178   6736  Z= 0.317
  Chirality :  0.042   0.166    782
  Planarity :  0.005   0.043    824
  Dihedral  :  6.418  58.006    728
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.93 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.35), residues: 613
  helix:  1.40 (0.25), residues: 452
  sheet:  None (None), residues: 0
  loop : -1.14 (0.50), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.020   0.002   TYR A 256 
 PHE   0.009   0.001   PHE A 534 
 TRP   0.012   0.001   TRP A 487 
 HIS   0.002   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4934)
  covalent geometry    : angle       0.60338 ( 6728)
  SS BOND              : bond        0.00443 (    4)
  SS BOND              : angle       1.66055 (    8)
  hydrogen bonds       : bond        0.04459 (  338)
  hydrogen bonds       : angle       5.31503 ( 1005)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A   91 SER cc_start: 0.9030 (m) cc_final: 0.8694 (p)
REVERT: A  191 THR cc_start: 0.8672 (m) cc_final: 0.8385 (m)
REVERT: A  216 MET cc_start: 0.8663 (ttp) cc_final: 0.8313 (ttp)
REVERT: A  323 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8930 (p)
REVERT: A  352 ARG cc_start: 0.7304 (ttm110) cc_final: 0.6921 (ttm170)
REVERT: A  382 MET cc_start: 0.8297 (mmm) cc_final: 0.8079 (mmm)
REVERT: A  412 ARG cc_start: 0.7400 (ttt180) cc_final: 0.6945 (ttp80)
REVERT: A  445 GLN cc_start: 0.7530 (mm110) cc_final: 0.7306 (mt0)
REVERT: A  455 TYR cc_start: 0.7870 (m-10) cc_final: 0.7396 (m-10)
REVERT: A  553 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7357 (ttp80)
REVERT: A  554 LYS cc_start: 0.8070 (pttt) cc_final: 0.7794 (pttm)
  outliers start: 7
  outliers final: 2
  residues processed: 73
  average time/residue: 0.0831
  time to fit residues: 7.5626
Evaluate side-chains
  71 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  642 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 55 optimal weight:   20.0000
   chunk 51 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0000
   chunk 54 optimal weight:    0.0980
   chunk 34 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.2190

-------------------------------------------------------------------------------
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 = 0.3248 r_free = 0.3248 target = 0.122030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.101889 restraints weight = 5158.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 1.26
r_work: 0.2894 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4938  Z= 0.126
  Angle     :  0.580   7.913   6736  Z= 0.298
  Chirality :  0.041   0.163    782
  Planarity :  0.005   0.043    824
  Dihedral  :  6.167  56.512    727
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.92 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.35), residues: 613
  helix:  1.60 (0.25), residues: 450
  sheet:  None (None), residues: 0
  loop : -0.81 (0.51), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.019   0.001   TYR A 256 
 PHE   0.009   0.001   PHE A 534 
 TRP   0.010   0.001   TRP A 487 
 HIS   0.002   0.001   HIS A  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4934)
  covalent geometry    : angle       0.57897 ( 6728)
  SS BOND              : bond        0.00379 (    4)
  SS BOND              : angle       1.05447 (    8)
  hydrogen bonds       : bond        0.04094 (  338)
  hydrogen bonds       : angle       5.15502 ( 1005)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8421 (m-10) cc_final: 0.7620 (m-10)
REVERT: A  191 THR cc_start: 0.8687 (m) cc_final: 0.8402 (m)
REVERT: A  216 MET cc_start: 0.8680 (ttp) cc_final: 0.8376 (ttp)
REVERT: A  323 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8984 (p)
REVERT: A  352 ARG cc_start: 0.7351 (ttm110) cc_final: 0.6974 (ttm170)
REVERT: A  363 ASN cc_start: 0.8659 (m-40) cc_final: 0.8456 (m110)
REVERT: A  382 MET cc_start: 0.8293 (mmm) cc_final: 0.8074 (mmm)
REVERT: A  412 ARG cc_start: 0.7448 (ttt180) cc_final: 0.7004 (ttp80)
REVERT: A  455 TYR cc_start: 0.8053 (m-10) cc_final: 0.7651 (m-10)
REVERT: A  553 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.7384 (ttp80)
REVERT: A  554 LYS cc_start: 0.8056 (pttt) cc_final: 0.7778 (pttm)
  outliers start: 8
  outliers final: 5
  residues processed: 75
  average time/residue: 0.0848
  time to fit residues: 7.8997
Evaluate side-chains
  73 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  642 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 32 optimal weight:    0.0870
   chunk 41 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0000
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.5364

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

Flipped N/Q/H residues before XYZ refinement:
A 445 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.125230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.105222 restraints weight = 5214.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.29
r_work: 0.2941 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4938  Z= 0.110
  Angle     :  0.560  10.852   6736  Z= 0.284
  Chirality :  0.040   0.159    782
  Planarity :  0.004   0.042    824
  Dihedral  :  5.963  54.988    727
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.52 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.36), residues: 613
  helix:  1.80 (0.25), residues: 452
  sheet:  None (None), residues: 0
  loop : -0.79 (0.51), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.019   0.001   TYR A 256 
 PHE   0.008   0.001   PHE A 534 
 TRP   0.010   0.001   TRP A  42 
 HIS   0.002   0.000   HIS A  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 4934)
  covalent geometry    : angle       0.55842 ( 6728)
  SS BOND              : bond        0.00512 (    4)
  SS BOND              : angle       1.40636 (    8)
  hydrogen bonds       : bond        0.03635 (  338)
  hydrogen bonds       : angle       4.97439 ( 1005)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8341 (m-10) cc_final: 0.7569 (m-10)
REVERT: A  191 THR cc_start: 0.8609 (m) cc_final: 0.8343 (m)
REVERT: A  216 MET cc_start: 0.8617 (ttp) cc_final: 0.8327 (ttp)
REVERT: A  323 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8908 (p)
REVERT: A  352 ARG cc_start: 0.7256 (ttm110) cc_final: 0.6967 (ttm170)
REVERT: A  363 ASN cc_start: 0.8571 (m-40) cc_final: 0.8350 (m110)
REVERT: A  382 MET cc_start: 0.8285 (mmm) cc_final: 0.8056 (mmm)
REVERT: A  412 ARG cc_start: 0.7459 (ttt180) cc_final: 0.6963 (ttp80)
REVERT: A  553 ARG cc_start: 0.7696 (mtp-110) cc_final: 0.7315 (ttp80)
REVERT: A  660 MET cc_start: 0.8558 (ttp) cc_final: 0.8316 (ttp)
  outliers start: 10
  outliers final: 4
  residues processed: 77
  average time/residue: 0.0672
  time to fit residues: 6.6268
Evaluate side-chains
  73 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  642 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 445 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.121907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.101502 restraints weight = 5238.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.29
r_work: 0.2887 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4938  Z= 0.131
  Angle     :  0.600  14.225   6736  Z= 0.300
  Chirality :  0.041   0.164    782
  Planarity :  0.005   0.043    824
  Dihedral  :  5.974  55.389    727
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.52 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.35), residues: 613
  helix:  1.72 (0.25), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.60 (0.52), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 130 
 TYR   0.017   0.001   TYR A 256 
 PHE   0.010   0.001   PHE A 534 
 TRP   0.010   0.001   TRP A 487 
 HIS   0.002   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4934)
  covalent geometry    : angle       0.59859 ( 6728)
  SS BOND              : bond        0.00449 (    4)
  SS BOND              : angle       1.43498 (    8)
  hydrogen bonds       : bond        0.04103 (  338)
  hydrogen bonds       : angle       5.06093 ( 1005)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8433 (m-10) cc_final: 0.7628 (m-10)
REVERT: A  191 THR cc_start: 0.8413 (m) cc_final: 0.8144 (m)
REVERT: A  216 MET cc_start: 0.8633 (ttp) cc_final: 0.8331 (ttp)
REVERT: A  323 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8975 (p)
REVERT: A  342 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8231 (mt-10)
REVERT: A  352 ARG cc_start: 0.7389 (ttm110) cc_final: 0.7050 (ttm170)
REVERT: A  382 MET cc_start: 0.8415 (mmm) cc_final: 0.8143 (mmm)
REVERT: A  412 ARG cc_start: 0.7479 (ttt180) cc_final: 0.7015 (ttp80)
REVERT: A  455 TYR cc_start: 0.8063 (m-10) cc_final: 0.7627 (m-10)
REVERT: A  553 ARG cc_start: 0.7743 (mtp-110) cc_final: 0.7377 (ttp80)
REVERT: A  554 LYS cc_start: 0.8066 (pttt) cc_final: 0.7812 (pttm)
  outliers start: 11
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0761
  time to fit residues: 7.4654
Evaluate side-chains
  76 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  642 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0470
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0970
   chunk 48 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
A 376 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.124748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.104557 restraints weight = 5240.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.29
r_work: 0.2932 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   4938  Z= 0.113
  Angle     :  0.567  13.296   6736  Z= 0.285
  Chirality :  0.040   0.162    782
  Planarity :  0.004   0.042    824
  Dihedral  :  5.872  54.605    727
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.52 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.35), residues: 613
  helix:  1.82 (0.25), residues: 455
  sheet:  None (None), residues: 0
  loop : -0.67 (0.51), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 130 
 TYR   0.018   0.001   TYR A 256 
 PHE   0.009   0.001   PHE A 534 
 TRP   0.008   0.001   TRP A 487 
 HIS   0.002   0.000   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 4934)
  covalent geometry    : angle       0.56471 ( 6728)
  SS BOND              : bond        0.00382 (    4)
  SS BOND              : angle       1.68164 (    8)
  hydrogen bonds       : bond        0.03676 (  338)
  hydrogen bonds       : angle       4.91791 ( 1005)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8365 (m-10) cc_final: 0.7593 (m-10)
REVERT: A  191 THR cc_start: 0.8564 (m) cc_final: 0.8318 (m)
REVERT: A  216 MET cc_start: 0.8579 (ttp) cc_final: 0.8277 (ttp)
REVERT: A  323 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8943 (p)
REVERT: A  352 ARG cc_start: 0.7222 (ttm110) cc_final: 0.6952 (ttm170)
REVERT: A  382 MET cc_start: 0.8394 (mmm) cc_final: 0.7929 (mmm)
REVERT: A  412 ARG cc_start: 0.7413 (ttt180) cc_final: 0.6959 (ttp80)
REVERT: A  553 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.7332 (ttp80)
REVERT: A  554 LYS cc_start: 0.8039 (pttt) cc_final: 0.7770 (pttm)
  outliers start: 12
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0737
  time to fit residues: 7.1735
Evaluate side-chains
  74 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  642 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 2 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 50 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.3236 r_free = 0.3236 target = 0.120941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.100625 restraints weight = 5286.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 1.28
r_work: 0.2878 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4938  Z= 0.141
  Angle     :  0.605  13.254   6736  Z= 0.307
  Chirality :  0.042   0.169    782
  Planarity :  0.005   0.043    824
  Dihedral  :  5.940  55.266    727
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.51 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.35), residues: 613
  helix:  1.72 (0.25), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.56 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 267 
 TYR   0.017   0.001   TYR A 256 
 PHE   0.011   0.001   PHE A 534 
 TRP   0.010   0.001   TRP A 487 
 HIS   0.003   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4934)
  covalent geometry    : angle       0.60280 ( 6728)
  SS BOND              : bond        0.00505 (    4)
  SS BOND              : angle       1.70830 (    8)
  hydrogen bonds       : bond        0.04251 (  338)
  hydrogen bonds       : angle       5.07289 ( 1005)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8465 (m-10) cc_final: 0.7658 (m-10)
REVERT: A  191 THR cc_start: 0.8482 (m) cc_final: 0.8210 (m)
REVERT: A  216 MET cc_start: 0.8685 (ttp) cc_final: 0.8361 (ttp)
REVERT: A  323 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8988 (p)
REVERT: A  352 ARG cc_start: 0.7434 (ttm110) cc_final: 0.7089 (ttm170)
REVERT: A  382 MET cc_start: 0.8521 (mmm) cc_final: 0.8287 (mmm)
REVERT: A  412 ARG cc_start: 0.7475 (ttt180) cc_final: 0.6645 (tmt-80)
REVERT: A  455 TYR cc_start: 0.8067 (m-10) cc_final: 0.7705 (m-10)
REVERT: A  553 ARG cc_start: 0.7825 (mtp-110) cc_final: 0.7430 (ttp80)
REVERT: A  554 LYS cc_start: 0.8103 (pttt) cc_final: 0.7827 (pttm)
  outliers start: 8
  outliers final: 7
  residues processed: 74
  average time/residue: 0.0709
  time to fit residues: 6.6482
Evaluate side-chains
  77 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  642 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 2 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0170
   chunk 29 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.6024

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

Flipped N/Q/H residues before XYZ refinement:
A 448 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.121057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.100474 restraints weight = 5232.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 1.30
r_work: 0.2884 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   4938  Z= 0.139
  Angle     :  0.605  13.227   6736  Z= 0.306
  Chirality :  0.042   0.172    782
  Planarity :  0.005   0.043    824
  Dihedral  :  5.955  55.426    727
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.71 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.35), residues: 613
  helix:  1.70 (0.25), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.53 (0.52), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.017   0.001   TYR A 256 
 PHE   0.011   0.001   PHE A 534 
 TRP   0.009   0.001   TRP A 487 
 HIS   0.003   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4934)
  covalent geometry    : angle       0.60313 ( 6728)
  SS BOND              : bond        0.00445 (    4)
  SS BOND              : angle       1.57629 (    8)
  hydrogen bonds       : bond        0.04213 (  338)
  hydrogen bonds       : angle       5.08818 ( 1005)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8426 (m-10) cc_final: 0.7622 (m-10)
REVERT: A  191 THR cc_start: 0.8519 (m) cc_final: 0.8238 (m)
REVERT: A  216 MET cc_start: 0.8653 (ttp) cc_final: 0.8313 (ttp)
REVERT: A  323 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8906 (p)
REVERT: A  352 ARG cc_start: 0.7281 (ttm110) cc_final: 0.6885 (ttm170)
REVERT: A  382 MET cc_start: 0.8462 (mmm) cc_final: 0.8224 (mmm)
REVERT: A  412 ARG cc_start: 0.7456 (ttt180) cc_final: 0.6551 (tmt-80)
REVERT: A  455 TYR cc_start: 0.7918 (m-10) cc_final: 0.7564 (m-10)
REVERT: A  553 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7377 (ttp80)
  outliers start: 9
  outliers final: 7
  residues processed: 74
  average time/residue: 0.0757
  time to fit residues: 6.9073
Evaluate side-chains
  78 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  642 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 2 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 448 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.123745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.103635 restraints weight = 5186.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 1.26
r_work: 0.2925 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4938  Z= 0.115
  Angle     :  0.570  12.727   6736  Z= 0.287
  Chirality :  0.040   0.167    782
  Planarity :  0.005   0.043    824
  Dihedral  :  5.843  54.413    727
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.92 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.35), residues: 613
  helix:  1.84 (0.25), residues: 454
  sheet:  None (None), residues: 0
  loop : -0.51 (0.52), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.018   0.001   TYR A 256 
 PHE   0.009   0.001   PHE A 534 
 TRP   0.008   0.001   TRP A 289 
 HIS   0.002   0.000   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4934)
  covalent geometry    : angle       0.56853 ( 6728)
  SS BOND              : bond        0.00311 (    4)
  SS BOND              : angle       1.30254 (    8)
  hydrogen bonds       : bond        0.03760 (  338)
  hydrogen bonds       : angle       4.91178 ( 1005)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8409 (m-10) cc_final: 0.7623 (m-10)
REVERT: A  191 THR cc_start: 0.8416 (m) cc_final: 0.8141 (m)
REVERT: A  216 MET cc_start: 0.8678 (ttp) cc_final: 0.8402 (ttp)
REVERT: A  323 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8955 (p)
REVERT: A  352 ARG cc_start: 0.7392 (ttm110) cc_final: 0.7080 (ttm170)
REVERT: A  382 MET cc_start: 0.8495 (mmm) cc_final: 0.8010 (mmm)
REVERT: A  412 ARG cc_start: 0.7463 (ttt180) cc_final: 0.6644 (tmt-80)
REVERT: A  553 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7367 (ttp80)
  outliers start: 9
  outliers final: 8
  residues processed: 75
  average time/residue: 0.0784
  time to fit residues: 7.4519
Evaluate side-chains
  79 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  642 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 48 optimal weight:    0.3980
   chunk 25 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 448 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.124903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.104876 restraints weight = 5238.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.28
r_work: 0.2942 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   4938  Z= 0.111
  Angle     :  0.558  12.497   6736  Z= 0.282
  Chirality :  0.040   0.174    782
  Planarity :  0.004   0.042    824
  Dihedral  :  5.751  53.379    727
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.92 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.35), residues: 613
  helix:  1.93 (0.25), residues: 454
  sheet:  None (None), residues: 0
  loop : -0.47 (0.52), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.017   0.001   TYR A 256 
 PHE   0.009   0.001   PHE A 534 
 TRP   0.009   0.001   TRP A 487 
 HIS   0.002   0.000   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 4934)
  covalent geometry    : angle       0.55664 ( 6728)
  SS BOND              : bond        0.00287 (    4)
  SS BOND              : angle       1.19272 (    8)
  hydrogen bonds       : bond        0.03585 (  338)
  hydrogen bonds       : angle       4.85150 ( 1005)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1120.23 seconds
wall clock time: 19 minutes 46.04 seconds (1186.04 seconds total)