Starting phenix.real_space_refine
on Tue Feb 11 07:54:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hg7_34737/02_2025/8hg7_34737.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hg7_34737/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hg7_34737/02_2025/8hg7_34737.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hg7_34737/02_2025/8hg7_34737.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hg7_34737/02_2025/8hg7_34737.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hg7_34737/02_2025/8hg7_34737.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.46, per 1000 atoms: 0.72
  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: 1.14
  Conformation dependent library (CDL) restraints added in 540.3 milliseconds
  

  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: 0.48
  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: 1.41

  Time building geometry restraints manager: 1.31 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:             0.090
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.620
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.920
-------------------------------------------------------------------------------
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      :  0.017   0.092   4934  Z= 1.083
  Angle     :  2.192  10.711   6728  Z= 1.612
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.29), 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
 TRP   0.022   0.004   TRP A 487 
 HIS   0.008   0.002   HIS A 309 
 PHE   0.022   0.004   PHE A 113 
 TYR   0.030   0.005   TYR A 128 
 ARG   0.007   0.001   ARG A 336 

*********************** 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  : 0.526 
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: 0.2625
  time to fit residues: 26.3956
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  : 0.530 
-------------------------------------------------------------------------------
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 51 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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
A 656 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.122846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.102330 restraints weight = 5127.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 1.29
r_work: 0.2901 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4934  Z= 0.190
  Angle     :  0.639   7.426   6728  Z= 0.335
  Chirality :  0.042   0.211    782
  Planarity :  0.005   0.039    824
  Dihedral  :  6.981  58.117    739
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.34), residues: 613
  helix:  0.88 (0.24), residues: 451
  sheet:  None (None), residues: 0
  loop : -1.22 (0.49), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  42 
 HIS   0.002   0.000   HIS A  80 
 PHE   0.011   0.001   PHE A  98 
 TYR   0.026   0.002   TYR A 256 
 ARG   0.004   0.000   ARG A 267 

*********************** 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
  87 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.540 
Fit side-chains
REVERT: A   91 SER cc_start: 0.8829 (m) cc_final: 0.8472 (p)
REVERT: A  191 THR cc_start: 0.8662 (m) cc_final: 0.8452 (m)
REVERT: A  216 MET cc_start: 0.8573 (ttp) cc_final: 0.8193 (ttp)
REVERT: A  323 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8900 (p)
REVERT: A  382 MET cc_start: 0.8386 (mmm) cc_final: 0.8118 (mmm)
REVERT: A  412 ARG cc_start: 0.7454 (ttt180) cc_final: 0.6869 (ttp80)
REVERT: A  445 GLN cc_start: 0.7558 (mm110) cc_final: 0.7342 (mt0)
REVERT: A  553 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7314 (ttp80)
REVERT: A  554 LYS cc_start: 0.8111 (pttt) cc_final: 0.7852 (pttm)
  outliers start: 8
  outliers final: 5
  residues processed: 82
  average time/residue: 0.2546
  time to fit residues: 24.9345
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  : 0.515 
-------------------------------------------------------------------------------
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 34 optimal weight:    0.5980
   chunk 56 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 2 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   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 557 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.123809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.103419 restraints weight = 5174.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.28
r_work: 0.2916 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4934  Z= 0.167
  Angle     :  0.574   7.201   6728  Z= 0.300
  Chirality :  0.040   0.162    782
  Planarity :  0.005   0.041    824
  Dihedral  :  6.333  57.355    728
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.73 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.35), residues: 613
  helix:  1.47 (0.25), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.96 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  42 
 HIS   0.002   0.000   HIS A  80 
 PHE   0.008   0.001   PHE A 534 
 TYR   0.021   0.001   TYR A 256 
 ARG   0.002   0.000   ARG A 267 

*********************** 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
  76 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A  191 THR cc_start: 0.8624 (m) cc_final: 0.8371 (m)
REVERT: A  216 MET cc_start: 0.8637 (ttp) cc_final: 0.8328 (ttp)
REVERT: A  323 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8916 (p)
REVERT: A  352 ARG cc_start: 0.7381 (ttm110) cc_final: 0.6953 (ttm170)
REVERT: A  382 MET cc_start: 0.8226 (mmm) cc_final: 0.7986 (mmm)
REVERT: A  412 ARG cc_start: 0.7383 (ttt180) cc_final: 0.6952 (ttp80)
REVERT: A  553 ARG cc_start: 0.7747 (mtp-110) cc_final: 0.7317 (ttp80)
  outliers start: 7
  outliers final: 2
  residues processed: 72
  average time/residue: 0.2216
  time to fit residues: 19.7033
Evaluate side-chains
  67 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
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 48 optimal weight:    0.0980
   chunk 55 optimal weight:   20.0000
   chunk 51 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 56 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3282 r_free = 0.3282 target = 0.124821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.104665 restraints weight = 5140.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.27
r_work: 0.2933 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4934  Z= 0.164
  Angle     :  0.554   7.094   6728  Z= 0.286
  Chirality :  0.040   0.158    782
  Planarity :  0.005   0.042    824
  Dihedral  :  6.056  55.856    727
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.72 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.35), residues: 613
  helix:  1.72 (0.25), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.83 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  42 
 HIS   0.002   0.000   HIS A  80 
 PHE   0.008   0.001   PHE A 534 
 TYR   0.020   0.001   TYR A 256 
 ARG   0.002   0.000   ARG A 267 

*********************** 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
  79 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8368 (m-10) cc_final: 0.7605 (m-10)
REVERT: A  191 THR cc_start: 0.8577 (m) cc_final: 0.8346 (m)
REVERT: A  216 MET cc_start: 0.8650 (ttp) cc_final: 0.8350 (ttp)
REVERT: A  323 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8976 (p)
REVERT: A  328 MET cc_start: 0.8656 (mtt) cc_final: 0.8271 (mtt)
REVERT: A  352 ARG cc_start: 0.7438 (ttm110) cc_final: 0.7050 (ttm170)
REVERT: A  382 MET cc_start: 0.8285 (mmm) cc_final: 0.8055 (mmm)
REVERT: A  412 ARG cc_start: 0.7443 (ttt180) cc_final: 0.6993 (ttp80)
REVERT: A  553 ARG cc_start: 0.7723 (mtp-110) cc_final: 0.7343 (ttp80)
  outliers start: 6
  outliers final: 3
  residues processed: 75
  average time/residue: 0.2185
  time to fit residues: 20.0247
Evaluate side-chains
  71 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
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  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 17 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 49 optimal weight:   20.0000
   chunk 35 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3239 r_free = 0.3239 target = 0.121370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.101016 restraints weight = 5247.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.28
r_work: 0.2882 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4934  Z= 0.213
  Angle     :  0.584   7.064   6728  Z= 0.303
  Chirality :  0.041   0.164    782
  Planarity :  0.005   0.043    824
  Dihedral  :  6.059  56.157    727
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.72 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.35), residues: 613
  helix:  1.68 (0.25), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.72 (0.52), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 487 
 HIS   0.002   0.001   HIS A 555 
 PHE   0.010   0.001   PHE A 534 
 TYR   0.019   0.001   TYR A 256 
 ARG   0.003   0.000   ARG A 130 

*********************** 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
  80 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.539 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8445 (m-10) cc_final: 0.7641 (m-10)
REVERT: A  191 THR cc_start: 0.8713 (m) cc_final: 0.8405 (m)
REVERT: A  198 MET cc_start: 0.8183 (mtt) cc_final: 0.7805 (mtt)
REVERT: A  216 MET cc_start: 0.8649 (ttp) cc_final: 0.8315 (ttp)
REVERT: A  323 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8985 (p)
REVERT: A  352 ARG cc_start: 0.7392 (ttm110) cc_final: 0.7003 (ttm170)
REVERT: A  363 ASN cc_start: 0.8651 (m-40) cc_final: 0.8429 (m110)
REVERT: A  382 MET cc_start: 0.8394 (mmm) cc_final: 0.8142 (mmm)
REVERT: A  412 ARG cc_start: 0.7507 (ttt180) cc_final: 0.7037 (ttp80)
REVERT: A  455 TYR cc_start: 0.8079 (m-10) cc_final: 0.7613 (m-10)
REVERT: A  553 ARG cc_start: 0.7770 (mtp-110) cc_final: 0.7397 (ttp80)
REVERT: A  554 LYS cc_start: 0.8092 (pttt) cc_final: 0.7830 (pttm)
REVERT: A  660 MET cc_start: 0.8642 (ttp) cc_final: 0.8415 (ttp)
  outliers start: 10
  outliers final: 6
  residues processed: 74
  average time/residue: 0.1958
  time to fit residues: 18.2571
Evaluate side-chains
  75 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
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  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 0 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3194 r_free = 0.3194 target = 0.117808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.097599 restraints weight = 5268.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2925 rms_B_bonded: 1.26
r_work: 0.2830 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4934  Z= 0.290
  Angle     :  0.624   6.984   6728  Z= 0.327
  Chirality :  0.044   0.167    782
  Planarity :  0.005   0.046    824
  Dihedral  :  6.203  57.259    727
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.72 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.35), residues: 613
  helix:  1.50 (0.25), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.79 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 487 
 HIS   0.003   0.001   HIS A 555 
 PHE   0.012   0.001   PHE A 666 
 TYR   0.018   0.002   TYR A 256 
 ARG   0.004   0.000   ARG A 130 

*********************** 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
  80 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8487 (m-10) cc_final: 0.7667 (m-10)
REVERT: A  191 THR cc_start: 0.8623 (m) cc_final: 0.8281 (m)
REVERT: A  198 MET cc_start: 0.8444 (mtt) cc_final: 0.8055 (mtt)
REVERT: A  216 MET cc_start: 0.8696 (ttp) cc_final: 0.8337 (ttp)
REVERT: A  323 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8968 (p)
REVERT: A  328 MET cc_start: 0.8703 (mtt) cc_final: 0.8335 (mtt)
REVERT: A  352 ARG cc_start: 0.7384 (ttm110) cc_final: 0.6924 (ttm170)
REVERT: A  382 MET cc_start: 0.8495 (mmm) cc_final: 0.8272 (mmm)
REVERT: A  412 ARG cc_start: 0.7501 (ttt180) cc_final: 0.7012 (ttp80)
REVERT: A  455 TYR cc_start: 0.8036 (m-10) cc_final: 0.7573 (m-10)
  outliers start: 11
  outliers final: 7
  residues processed: 76
  average time/residue: 0.1972
  time to fit residues: 18.8795
Evaluate side-chains
  75 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
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  359 VAL
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 2 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.122630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.102624 restraints weight = 5164.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 1.26
r_work: 0.2904 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4934  Z= 0.180
  Angle     :  0.555   6.944   6728  Z= 0.290
  Chirality :  0.040   0.163    782
  Planarity :  0.005   0.043    824
  Dihedral  :  5.984  55.423    727
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.52 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.35), residues: 613
  helix:  1.71 (0.25), residues: 452
  sheet:  None (None), residues: 0
  loop : -0.54 (0.52), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  65 
 HIS   0.002   0.001   HIS A 555 
 PHE   0.009   0.001   PHE A 534 
 TYR   0.019   0.001   TYR A 256 
 ARG   0.003   0.000   ARG A 130 

*********************** 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
  82 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8418 (m-10) cc_final: 0.7632 (m-10)
REVERT: A  191 THR cc_start: 0.8439 (m) cc_final: 0.8165 (m)
REVERT: A  216 MET cc_start: 0.8636 (ttp) cc_final: 0.8323 (ttp)
REVERT: A  323 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8937 (p)
REVERT: A  342 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8256 (mt-10)
REVERT: A  382 MET cc_start: 0.8380 (mmm) cc_final: 0.8169 (mmm)
REVERT: A  412 ARG cc_start: 0.7466 (ttt180) cc_final: 0.7006 (ttp80)
REVERT: A  455 TYR cc_start: 0.8036 (m-10) cc_final: 0.7623 (m-10)
REVERT: A  553 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7180 (ttp80)
  outliers start: 11
  outliers final: 7
  residues processed: 78
  average time/residue: 0.1943
  time to fit residues: 19.1392
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  : 0.516 
-------------------------------------------------------------------------------
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  342 GLU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  364 ILE
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 8 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 56 optimal weight:    0.4980
   chunk 3 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3254 r_free = 0.3254 target = 0.122502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.102544 restraints weight = 5215.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.25
r_work: 0.2908 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4934  Z= 0.186
  Angle     :  0.555   6.958   6728  Z= 0.291
  Chirality :  0.041   0.170    782
  Planarity :  0.005   0.043    824
  Dihedral  :  5.920  54.824    727
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.35), residues: 613
  helix:  1.72 (0.25), residues: 455
  sheet:  None (None), residues: 0
  loop : -0.70 (0.51), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  42 
 HIS   0.002   0.001   HIS A 555 
 PHE   0.010   0.001   PHE A 534 
 TYR   0.017   0.001   TYR A 256 
 ARG   0.003   0.000   ARG A 553 

*********************** 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
  82 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8428 (m-10) cc_final: 0.7629 (m-10)
REVERT: A  191 THR cc_start: 0.8457 (m) cc_final: 0.8190 (m)
REVERT: A  216 MET cc_start: 0.8660 (ttp) cc_final: 0.8326 (ttp)
REVERT: A  323 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8971 (p)
REVERT: A  352 ARG cc_start: 0.7379 (ttm110) cc_final: 0.7057 (ttm170)
REVERT: A  382 MET cc_start: 0.8334 (mmm) cc_final: 0.8111 (mmm)
REVERT: A  412 ARG cc_start: 0.7461 (ttt180) cc_final: 0.7004 (ttp80)
REVERT: A  455 TYR cc_start: 0.8049 (m-10) cc_final: 0.7659 (m-10)
REVERT: A  553 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.7195 (ttp80)
  outliers start: 11
  outliers final: 7
  residues processed: 79
  average time/residue: 0.1964
  time to fit residues: 19.4212
Evaluate side-chains
  76 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
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  364 ILE
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 34 optimal weight:    4.9990
   chunk 55 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3242 r_free = 0.3242 target = 0.121504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.101544 restraints weight = 5195.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 1.25
r_work: 0.2892 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4934  Z= 0.207
  Angle     :  0.567   7.014   6728  Z= 0.298
  Chirality :  0.041   0.174    782
  Planarity :  0.005   0.044    824
  Dihedral  :  5.921  54.861    727
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.12 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.35), residues: 613
  helix:  1.71 (0.25), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.56 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 487 
 HIS   0.002   0.001   HIS A 555 
 PHE   0.010   0.001   PHE A 534 
 TYR   0.017   0.001   TYR A 256 
 ARG   0.003   0.000   ARG A 553 

*********************** 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: 8
    poor density    : 70
  time to evaluate  : 0.532 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8453 (m-10) cc_final: 0.7650 (m-10)
REVERT: A  191 THR cc_start: 0.8519 (m) cc_final: 0.8238 (m)
REVERT: A  216 MET cc_start: 0.8662 (ttp) cc_final: 0.8330 (ttp)
REVERT: A  323 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8961 (p)
REVERT: A  352 ARG cc_start: 0.7400 (ttm110) cc_final: 0.7056 (ttm170)
REVERT: A  382 MET cc_start: 0.8438 (mmm) cc_final: 0.8207 (mmm)
REVERT: A  412 ARG cc_start: 0.7462 (ttt180) cc_final: 0.6627 (tmt-80)
REVERT: A  455 TYR cc_start: 0.8019 (m-10) cc_final: 0.7638 (m-10)
REVERT: A  553 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7208 (ttp80)
  outliers start: 8
  outliers final: 7
  residues processed: 75
  average time/residue: 0.2058
  time to fit residues: 19.3399
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  : 0.511 
-------------------------------------------------------------------------------
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  342 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3209 r_free = 0.3209 target = 0.119047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.098971 restraints weight = 5279.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 1.27
r_work: 0.2855 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2732 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4934  Z= 0.247
  Angle     :  0.597   7.013   6728  Z= 0.313
  Chirality :  0.043   0.177    782
  Planarity :  0.005   0.044    824
  Dihedral  :  6.015  55.523    727
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.12 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.35), residues: 613
  helix:  1.60 (0.25), residues: 453
  sheet:  None (None), residues: 0
  loop : -0.62 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 487 
 HIS   0.003   0.001   HIS A 555 
 PHE   0.011   0.001   PHE A 534 
 TYR   0.016   0.001   TYR A 256 
 ARG   0.003   0.000   ARG A 553 

********************** 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
  81 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  150 TYR cc_start: 0.8476 (m-10) cc_final: 0.7673 (m-10)
REVERT: A  191 THR cc_start: 0.8637 (m) cc_final: 0.8332 (m)
REVERT: A  216 MET cc_start: 0.8690 (ttp) cc_final: 0.8333 (ttp)
REVERT: A  323 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8962 (p)
REVERT: A  328 MET cc_start: 0.8656 (mtt) cc_final: 0.8273 (mtt)
REVERT: A  382 MET cc_start: 0.8438 (mmm) cc_final: 0.8210 (mmm)
REVERT: A  412 ARG cc_start: 0.7472 (ttt180) cc_final: 0.6981 (ttp80)
REVERT: A  455 TYR cc_start: 0.7989 (m-10) cc_final: 0.7609 (m-10)
REVERT: A  553 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.7254 (ttp80)
REVERT: A  660 MET cc_start: 0.8466 (ttp) cc_final: 0.7953 (tmm)
  outliers start: 12
  outliers final: 9
  residues processed: 76
  average time/residue: 0.2157
  time to fit residues: 20.4868
Evaluate side-chains
  78 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
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  359 VAL
Chi-restraints excluded: chain A residue  364 ILE
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 11 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3260 r_free = 0.3260 target = 0.122904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.103011 restraints weight = 5237.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.28
r_work: 0.2912 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4934  Z= 0.179
  Angle     :  0.552   6.935   6728  Z= 0.290
  Chirality :  0.040   0.167    782
  Planarity :  0.005   0.043    824
  Dihedral  :  5.869  54.075    727
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.72 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.35), residues: 613
  helix:  1.78 (0.25), residues: 452
  sheet:  None (None), residues: 0
  loop : -0.48 (0.52), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 289 
 HIS   0.002   0.000   HIS A 555 
 PHE   0.009   0.001   PHE A 534 
 TYR   0.018   0.001   TYR A 256 
 ARG   0.002   0.000   ARG A 553 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2427.76 seconds
wall clock time: 43 minutes 39.47 seconds (2619.47 seconds total)