Starting phenix.real_space_refine
on Wed Feb  4 01:44:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xzk_72359/02_2026/9xzk_72359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xzk_72359/02_2026/9xzk_72359.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xzk_72359/02_2026/9xzk_72359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xzk_72359/02_2026/9xzk_72359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xzk_72359/02_2026/9xzk_72359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xzk_72359/02_2026/9xzk_72359.cif"
  }
  resolution = 3.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
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: 5
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2531      2.51       5
     N     678      2.21       5
     O     756      1.98       5
     H    4033      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8018
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 7736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 7736
          Classifications: {'peptide': 476}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 465}
    Chain: "R"
      Number of atoms: 282
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 282
          Classifications: {'peptide': 16}
          Link IDs: {'TRANS': 15}
  Time building chain proxies: 1.48, per 1000 atoms: 0.18
  Number of scatterers: 8018
  At special positions: 0
  Unit cell: (86.708, 99.796, 84.254, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     O     756      8.00
     N     678      7.00
     C    2531      6.00
     H    4033      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.57
  Conformation dependent library (CDL) restraints added in 107.6 milliseconds
  

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  954

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 4 sheets defined
      66.7% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'C' and resid 301 through 314
      removed outlier: 3.838A  pdb=" N   THR C 305 " --> pdb=" O   GLU C 301 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN C 308 " --> pdb=" O   HIS C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 315 through 328
      removed outlier: 3.861A  pdb=" N   LEU C 319 " --> pdb=" O   LYS C 315 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   GLY C 320 " --> pdb=" O   ASN C 316 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   ARG C 321 " --> pdb=" O   GLU C 317 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ARG C 328 " --> pdb=" O   ASN C 324 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 356
      removed outlier: 4.119A  pdb=" N   LEU C 336 " --> pdb=" O   GLY C 332 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   CYS C 355 " --> pdb=" O   ALA C 351 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY C 356 " --> pdb=" O   ILE C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 357 through 361
    Processing helix  chain 'C' and resid 362 through 384
    Processing helix  chain 'C' and resid 388 through 404
      removed outlier: 3.687A  pdb=" N   ASN C 404 " --> pdb=" O   GLY C 400 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 413
    Processing helix  chain 'C' and resid 416 through 431
    Processing helix  chain 'C' and resid 438 through 454
    Processing helix  chain 'C' and resid 458 through 477
      removed outlier: 3.538A  pdb=" N   PHE C 462 " --> pdb=" O   ASP C 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 481 through 497
    Processing helix  chain 'C' and resid 497 through 527
      removed outlier: 3.604A  pdb=" N   THR C 501 " --> pdb=" O   GLY C 497 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   LYS C 503 " --> pdb=" O   GLU C 499 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   LEU C 504 " --> pdb=" O   TYR C 500 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   LYS C 523 " --> pdb=" O   GLU C 519 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   HIS C 524 " --> pdb=" O   GLN C 520 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU C 525 " --> pdb=" O   PHE C 521 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 574
    Processing helix  chain 'C' and resid 583 through 586
    Processing helix  chain 'C' and resid 604 through 613
      removed outlier: 3.668A  pdb=" N   GLN C 613 " --> pdb=" O   ALA C 609 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 614 through 616
      No H-bonds generated for 'chain 'C' and resid 614 through 616'
    Processing helix  chain 'C' and resid 622 through 630
    Processing helix  chain 'C' and resid 632 through 646
      removed outlier: 3.659A  pdb=" N   SER C 646 " --> pdb=" O   ILE C 642 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 688 through 723
      removed outlier: 3.957A  pdb=" N   GLN C 692 " --> pdb=" O   MET C 688 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   LYS C 693 " --> pdb=" O   GLU C 689 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 727 through 739
    Processing helix  chain 'C' and resid 745 through 759
    Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541
      removed outlier: 4.006A  pdb=" N   ALA R  31 " --> pdb=" O   GLN C 538 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 534 through 541
      removed outlier: 4.006A  pdb=" N   ALA R  31 " --> pdb=" O   GLN C 538 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   VAL R  24 " --> pdb=" O   VAL C 591 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   VAL C 591 " --> pdb=" O   VAL R  24 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LYS R  26 " --> pdb=" O   GLU C 589 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 619 through 621
    Processing sheet with id=AA4, first strand: chain 'C' and resid 724 through 726

    259 hydrogen bonds defined for protein.
    759 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: 1.75

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4026
        1.03 -     1.23: 7
        1.23 -     1.42: 1656
        1.42 -     1.61: 2361
        1.61 -     1.81: 33
  Bond restraints: 8083
  Sorted by residual:
  bond pdb=" N   GLN C 548 "
       pdb=" CA  GLN C 548 "
    ideal  model  delta    sigma   weight residual
    1.468  1.457  0.011 1.24e-02 6.50e+03 8.56e-01
  bond pdb=" C   GLY C 334 "
       pdb=" O   GLY C 334 "
    ideal  model  delta    sigma   weight residual
    1.234  1.242 -0.008 1.21e-02 6.83e+03 4.66e-01
  bond pdb=" CB  ASN C 518 "
       pdb=" CG  ASN C 518 "
    ideal  model  delta    sigma   weight residual
    1.516  1.500  0.016 2.50e-02 1.60e+03 4.13e-01
  bond pdb=" CB  ASP C 510 "
       pdb=" CG  ASP C 510 "
    ideal  model  delta    sigma   weight residual
    1.516  1.501  0.015 2.50e-02 1.60e+03 3.77e-01
  bond pdb=" CB  TRP C 581 "
       pdb=" CG  TRP C 581 "
    ideal  model  delta    sigma   weight residual
    1.498  1.480  0.018 3.10e-02 1.04e+03 3.42e-01
  ... (remaining 8078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.81: 13217
        0.81 -     1.62: 1337
        1.62 -     2.43: 72
        2.43 -     3.24: 9
        3.24 -     4.05: 8
  Bond angle restraints: 14643
  Sorted by residual:
  angle pdb=" CA  TYR C 377 "
        pdb=" CB  TYR C 377 "
        pdb=" CG  TYR C 377 "
      ideal   model   delta    sigma   weight residual
     113.90  109.85    4.05 1.80e+00 3.09e-01 5.07e+00
  angle pdb=" C   ARG C 722 "
        pdb=" N   LYS C 723 "
        pdb=" CA  LYS C 723 "
      ideal   model   delta    sigma   weight residual
     121.54  125.35   -3.81 1.91e+00 2.74e-01 3.98e+00
  angle pdb=" C   ARG C 401 "
        pdb=" N   PHE C 402 "
        pdb=" CA  PHE C 402 "
      ideal   model   delta    sigma   weight residual
     121.66  118.37    3.29 1.76e+00 3.23e-01 3.49e+00
  angle pdb=" C   LYS C 376 "
        pdb=" N   TYR C 377 "
        pdb=" CA  TYR C 377 "
      ideal   model   delta    sigma   weight residual
     120.68  117.98    2.70 1.70e+00 3.46e-01 2.52e+00
  angle pdb=" C   LYS C 647 "
        pdb=" CA  LYS C 647 "
        pdb=" CB  LYS C 647 "
      ideal   model   delta    sigma   weight residual
     110.65  107.87    2.78 1.95e+00 2.63e-01 2.04e+00
  ... (remaining 14638 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.91: 3578
       15.91 -    31.81: 134
       31.81 -    47.72: 25
       47.72 -    63.62: 20
       63.62 -    79.53: 3
  Dihedral angle restraints: 3760
    sinusoidal: 2069
      harmonic: 1691
  Sorted by residual:
  dihedral pdb=" CA  ARG C 424 "
           pdb=" CB  ARG C 424 "
           pdb=" CG  ARG C 424 "
           pdb=" CD  ARG C 424 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.40   57.40     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" N   PHE C 508 "
           pdb=" CA  PHE C 508 "
           pdb=" CB  PHE C 508 "
           pdb=" CG  PHE C 508 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -132.45  -47.55     3      1.50e+01 4.44e-03 8.51e+00
  dihedral pdb=" N   MET C 507 "
           pdb=" CA  MET C 507 "
           pdb=" CB  MET C 507 "
           pdb=" CG  MET C 507 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.36   47.36     3      1.50e+01 4.44e-03 8.48e+00
  ... (remaining 3757 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 435
       0.029 -    0.058: 118
       0.058 -    0.086: 41
       0.086 -    0.115: 17
       0.115 -    0.144: 3
  Chirality restraints: 614
  Sorted by residual:
  chirality pdb=" CA  ILE C 669 "
            pdb=" N   ILE C 669 "
            pdb=" C   ILE C 669 "
            pdb=" CB  ILE C 669 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  VAL C 724 "
            pdb=" N   VAL C 724 "
            pdb=" C   VAL C 724 "
            pdb=" CB  VAL C 724 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  VAL C 591 "
            pdb=" N   VAL C 591 "
            pdb=" C   VAL C 591 "
            pdb=" CB  VAL C 591 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.47e-01
  ... (remaining 611 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 377 "   -0.011 2.00e-02 2.50e+03   5.53e-03 9.18e-01
        pdb=" CG  TYR C 377 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 377 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 377 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 377 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 377 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 377 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 377 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 377 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 377 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 377 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 377 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 402 "   -0.007 2.00e-02 2.50e+03   4.62e-03 6.39e-01
        pdb=" CG  PHE C 402 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 402 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 402 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 402 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 402 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 402 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 PHE C 402 "    0.000 2.00e-02 2.50e+03
        pdb=" HD2 PHE C 402 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 PHE C 402 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE C 402 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ  PHE C 402 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 664 "    0.013 5.00e-02 4.00e+02   1.97e-02 6.19e-01
        pdb=" N   PRO C 665 "   -0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO C 665 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO C 665 "    0.011 5.00e-02 4.00e+02
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.40: 3379
        2.40 -     2.95: 19036
        2.95 -     3.50: 19675
        3.50 -     4.05: 25335
        4.05 -     4.60: 39947
  Nonbonded interactions: 107372
  Sorted by model distance:
  nonbonded pdb=" H   ASN C 406 "
            pdb=" HG1 THR C 409 "
     model   vdw
     1.845 2.100
  nonbonded pdb=" HG1 THR C 592 "
            pdb=" H   TYR C 599 "
     model   vdw
     1.878 2.100
  nonbonded pdb=" H   SER C 541 "
            pdb=" HG  SER C 541 "
     model   vdw
     1.902 2.100
  nonbonded pdb="HE21 GLN C 602 "
            pdb="HH21 ARG C 681 "
     model   vdw
     1.902 2.100
  nonbonded pdb=" H   SER C 542 "
            pdb=" HG  SER C 542 "
     model   vdw
     1.974 2.100
  ... (remaining 107367 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             14.470
  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:             0.040
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.690
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
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      :  0.003   0.019   4050  Z= 0.169
  Angle     :  0.426   4.053   5453  Z= 0.252
  Chirality :  0.034   0.144    614
  Planarity :  0.002   0.020    696
  Dihedral  :  8.998  79.527   1546
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 1.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  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 are not related in a simple way.
  whole:  2.81 (0.39), residues: 488
  helix:  2.84 (0.30), residues: 297
  sheet:  0.05 (1.30), residues: 20
  loop :  0.37 (0.48), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 707 
 TYR   0.015   0.001   TYR C 377 
 PHE   0.014   0.001   PHE C 402 
 TRP   0.004   0.001   TRP R  33 
 HIS   0.005   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4050)
  covalent geometry    : angle       0.42552 ( 5453)
  hydrogen bonds       : bond        0.09809 (  252)
  hydrogen bonds       : angle       5.42534 (  759)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  365 MET cc_start: 0.8275 (ttm) cc_final: 0.7930 (tpp)
REVERT: R   25 LYS cc_start: 0.8435 (tttt) cc_final: 0.8040 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.2170
  time to fit residues: 16.2004
Evaluate side-chains
  38 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 22 optimal weight:    0.4980
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
C 518 ASN
C 524 HIS
C 584 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.088872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.072872 restraints weight = 39593.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.075612 restraints weight = 16309.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.077320 restraints weight = 9291.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.078391 restraints weight = 6412.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.079038 restraints weight = 5098.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4050  Z= 0.135
  Angle     :  0.440   4.523   5453  Z= 0.247
  Chirality :  0.034   0.141    614
  Planarity :  0.002   0.021    696
  Dihedral  :  3.473  14.336    528
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.56 %
    Favored  : 92.76 %
  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 are not related in a simple way.
  whole:  2.86 (0.39), residues: 488
  helix:  2.86 (0.29), residues: 297
  sheet: -0.20 (1.27), residues: 20
  loop :  0.45 (0.50), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 506 
 TYR   0.015   0.001   TYR C 377 
 PHE   0.012   0.001   PHE C 402 
 TRP   0.004   0.001   TRP C 545 
 HIS   0.008   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4050)
  covalent geometry    : angle       0.44028 ( 5453)
  hydrogen bonds       : bond        0.04150 (  252)
  hydrogen bonds       : angle       4.53458 (  759)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  365 MET cc_start: 0.8411 (ttm) cc_final: 0.8180 (tpp)
REVERT: C  562 SER cc_start: 0.9144 (m) cc_final: 0.8762 (p)
REVERT: R   25 LYS cc_start: 0.8390 (tttt) cc_final: 0.7971 (tppt)
  outliers start: 3
  outliers final: 3
  residues processed: 38
  average time/residue: 0.1923
  time to fit residues: 8.8994
Evaluate side-chains
  38 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  507 MET
Chi-restraints excluded: chain C residue  508 PHE
Chi-restraints excluded: chain C residue  711 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0980
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0570
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
C 518 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.089067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.072672 restraints weight = 39505.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.075522 restraints weight = 16016.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.077312 restraints weight = 8974.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.078424 restraints weight = 6220.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.078955 restraints weight = 4976.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4050  Z= 0.115
  Angle     :  0.424   5.295   5453  Z= 0.234
  Chirality :  0.034   0.142    614
  Planarity :  0.002   0.025    696
  Dihedral  :  3.399  13.211    528
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  5.88 %
    Favored  : 93.21 %
  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 are not related in a simple way.
  whole:  2.85 (0.39), residues: 488
  helix:  2.85 (0.29), residues: 301
  sheet: -0.21 (1.26), residues: 20
  loop :  0.39 (0.50), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 506 
 TYR   0.013   0.001   TYR C 377 
 PHE   0.011   0.001   PHE C 566 
 TRP   0.003   0.001   TRP C 545 
 HIS   0.004   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 4050)
  covalent geometry    : angle       0.42425 ( 5453)
  hydrogen bonds       : bond        0.03806 (  252)
  hydrogen bonds       : angle       4.30964 (  759)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  328 ARG cc_start: 0.5226 (tmt170) cc_final: 0.4891 (tmt170)
REVERT: C  365 MET cc_start: 0.8401 (ttm) cc_final: 0.8157 (tpp)
REVERT: R   25 LYS cc_start: 0.8379 (tttt) cc_final: 0.7977 (tppt)
  outliers start: 4
  outliers final: 3
  residues processed: 37
  average time/residue: 0.1472
  time to fit residues: 6.8253
Evaluate side-chains
  37 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  507 MET
Chi-restraints excluded: chain C residue  508 PHE
Chi-restraints excluded: chain C residue  537 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0770
   chunk 2 optimal weight:    0.1980
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.5342

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

Flipped N/Q/H residues before XYZ refinement:
C 518 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.088702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.072174 restraints weight = 40529.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.075023 restraints weight = 16469.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.076815 restraints weight = 9269.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.077925 restraints weight = 6431.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.078589 restraints weight = 5155.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4050  Z= 0.124
  Angle     :  0.416   5.032   5453  Z= 0.231
  Chirality :  0.034   0.140    614
  Planarity :  0.002   0.021    696
  Dihedral  :  3.381  13.337    528
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  5.43 %
    Favored  : 93.44 %
  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 are not related in a simple way.
  whole:  2.97 (0.39), residues: 488
  helix:  2.97 (0.29), residues: 297
  sheet: -0.26 (1.24), residues: 20
  loop :  0.47 (0.49), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 707 
 TYR   0.014   0.001   TYR C 377 
 PHE   0.012   0.001   PHE C 566 
 TRP   0.003   0.001   TRP R  33 
 HIS   0.004   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4050)
  covalent geometry    : angle       0.41598 ( 5453)
  hydrogen bonds       : bond        0.03694 (  252)
  hydrogen bonds       : angle       4.22988 (  759)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  328 ARG cc_start: 0.5015 (tmt170) cc_final: 0.4495 (ttt-90)
REVERT: C  365 MET cc_start: 0.8381 (ttm) cc_final: 0.8034 (tpp)
REVERT: R   25 LYS cc_start: 0.8418 (tttt) cc_final: 0.7990 (tppt)
  outliers start: 5
  outliers final: 5
  residues processed: 39
  average time/residue: 0.1616
  time to fit residues: 7.9756
Evaluate side-chains
  40 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  507 MET
Chi-restraints excluded: chain C residue  508 PHE
Chi-restraints excluded: chain C residue  537 ILE
Chi-restraints excluded: chain C residue  562 SER
Chi-restraints excluded: chain C residue  711 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 1 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0060
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0870
   overall best weight:    0.4374

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

Flipped N/Q/H residues before XYZ refinement:
C 518 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.089057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.072514 restraints weight = 39801.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.075372 restraints weight = 16295.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.077162 restraints weight = 9148.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.078270 restraints weight = 6368.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.078825 restraints weight = 5088.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4050  Z= 0.108
  Angle     :  0.409   5.544   5453  Z= 0.224
  Chirality :  0.034   0.141    614
  Planarity :  0.002   0.021    696
  Dihedral  :  3.329  12.992    528
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  6.33 %
    Favored  : 92.31 %
  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 are not related in a simple way.
  whole:  3.05 (0.39), residues: 488
  helix:  2.99 (0.29), residues: 297
  sheet: -0.17 (1.24), residues: 20
  loop :  0.59 (0.50), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 565 
 TYR   0.013   0.001   TYR C 377 
 PHE   0.011   0.001   PHE C 566 
 TRP   0.003   0.001   TRP R  33 
 HIS   0.004   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 4050)
  covalent geometry    : angle       0.40878 ( 5453)
  hydrogen bonds       : bond        0.03567 (  252)
  hydrogen bonds       : angle       4.12904 (  759)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  328 ARG cc_start: 0.5054 (tmt170) cc_final: 0.4478 (ttt-90)
REVERT: C  365 MET cc_start: 0.8352 (ttm) cc_final: 0.8008 (tpp)
REVERT: R   25 LYS cc_start: 0.8398 (tttt) cc_final: 0.7954 (tppt)
  outliers start: 6
  outliers final: 5
  residues processed: 38
  average time/residue: 0.1801
  time to fit residues: 8.5820
Evaluate side-chains
  41 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  507 MET
Chi-restraints excluded: chain C residue  508 PHE
Chi-restraints excluded: chain C residue  537 ILE
Chi-restraints excluded: chain C residue  597 ASN
Chi-restraints excluded: chain C residue  711 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C 518 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.088130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.071327 restraints weight = 40683.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.074053 restraints weight = 16953.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.075732 restraints weight = 9753.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.076785 restraints weight = 6910.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.077421 restraints weight = 5605.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4050  Z= 0.167
  Angle     :  0.439   5.817   5453  Z= 0.247
  Chirality :  0.034   0.137    614
  Planarity :  0.003   0.029    696
  Dihedral  :  3.425  14.311    528
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  6.33 %
    Favored  : 92.31 %
  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 are not related in a simple way.
  whole:  2.85 (0.38), residues: 488
  helix:  2.89 (0.29), residues: 296
  sheet: -0.44 (1.18), residues: 20
  loop :  0.42 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 707 
 TYR   0.015   0.001   TYR C 377 
 PHE   0.013   0.001   PHE C 566 
 TRP   0.004   0.001   TRP R  33 
 HIS   0.005   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4050)
  covalent geometry    : angle       0.43900 ( 5453)
  hydrogen bonds       : bond        0.03767 (  252)
  hydrogen bonds       : angle       4.24938 (  759)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  328 ARG cc_start: 0.4708 (tmt170) cc_final: 0.4308 (ttt180)
REVERT: C  365 MET cc_start: 0.8368 (ttm) cc_final: 0.8011 (tpp)
REVERT: R   25 LYS cc_start: 0.8440 (tttt) cc_final: 0.8006 (tppt)
  outliers start: 6
  outliers final: 6
  residues processed: 39
  average time/residue: 0.1705
  time to fit residues: 8.3304
Evaluate side-chains
  41 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  507 MET
Chi-restraints excluded: chain C residue  508 PHE
Chi-restraints excluded: chain C residue  537 ILE
Chi-restraints excluded: chain C residue  597 ASN
Chi-restraints excluded: chain C residue  711 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 518 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.088419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.071635 restraints weight = 41211.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.074353 restraints weight = 17020.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.076049 restraints weight = 9770.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.077029 restraints weight = 6884.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.077696 restraints weight = 5666.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
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   0.017   4050  Z= 0.142
  Angle     :  0.423   5.139   5453  Z= 0.236
  Chirality :  0.034   0.149    614
  Planarity :  0.002   0.027    696
  Dihedral  :  3.414  13.753    528
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  6.33 %
    Favored  : 91.86 %
  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 are not related in a simple way.
  whole:  2.86 (0.38), residues: 488
  helix:  2.89 (0.29), residues: 296
  sheet: -0.46 (1.17), residues: 20
  loop :  0.45 (0.50), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 565 
 TYR   0.015   0.001   TYR C 377 
 PHE   0.011   0.001   PHE C 566 
 TRP   0.004   0.001   TRP R  33 
 HIS   0.005   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4050)
  covalent geometry    : angle       0.42286 ( 5453)
  hydrogen bonds       : bond        0.03698 (  252)
  hydrogen bonds       : angle       4.14760 (  759)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  328 ARG cc_start: 0.4640 (tmt170) cc_final: 0.4380 (ttt180)
REVERT: C  365 MET cc_start: 0.8409 (ttm) cc_final: 0.8039 (tpp)
REVERT: R   25 LYS cc_start: 0.8438 (tttt) cc_final: 0.8009 (tppt)
  outliers start: 8
  outliers final: 7
  residues processed: 42
  average time/residue: 0.1690
  time to fit residues: 8.9731
Evaluate side-chains
  42 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  507 MET
Chi-restraints excluded: chain C residue  508 PHE
Chi-restraints excluded: chain C residue  537 ILE
Chi-restraints excluded: chain C residue  597 ASN
Chi-restraints excluded: chain C residue  711 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0050
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
C 518 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.088204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.071947 restraints weight = 40313.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.074664 restraints weight = 16139.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.076351 restraints weight = 9045.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.077379 restraints weight = 6288.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.077928 restraints weight = 5054.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4050  Z= 0.141
  Angle     :  0.428   6.540   5453  Z= 0.237
  Chirality :  0.034   0.148    614
  Planarity :  0.002   0.030    696
  Dihedral  :  3.392  13.623    528
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  6.56 %
    Favored  : 91.63 %
  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 are not related in a simple way.
  whole:  2.85 (0.38), residues: 488
  helix:  2.89 (0.29), residues: 296
  sheet: -0.46 (1.18), residues: 20
  loop :  0.43 (0.50), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 328 
 TYR   0.015   0.001   TYR C 377 
 PHE   0.012   0.001   PHE C 566 
 TRP   0.003   0.001   TRP R  33 
 HIS   0.005   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4050)
  covalent geometry    : angle       0.42758 ( 5453)
  hydrogen bonds       : bond        0.03677 (  252)
  hydrogen bonds       : angle       4.13058 (  759)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  328 ARG cc_start: 0.4483 (tmt170) cc_final: 0.4246 (ttt180)
REVERT: C  365 MET cc_start: 0.8407 (ttm) cc_final: 0.8036 (tpp)
REVERT: R   25 LYS cc_start: 0.8435 (tttt) cc_final: 0.7996 (tppt)
  outliers start: 8
  outliers final: 8
  residues processed: 40
  average time/residue: 0.1668
  time to fit residues: 8.5099
Evaluate side-chains
  42 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  507 MET
Chi-restraints excluded: chain C residue  508 PHE
Chi-restraints excluded: chain C residue  537 ILE
Chi-restraints excluded: chain C residue  597 ASN
Chi-restraints excluded: chain C residue  626 THR
Chi-restraints excluded: chain C residue  711 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0060
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0030
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.4606

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

Flipped N/Q/H residues before XYZ refinement:
C 518 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.088874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.072018 restraints weight = 40651.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.074790 restraints weight = 16903.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.076502 restraints weight = 9667.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.077557 restraints weight = 6822.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.078105 restraints weight = 5531.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4050  Z= 0.114
  Angle     :  0.429   7.278   5453  Z= 0.231
  Chirality :  0.034   0.156    614
  Planarity :  0.002   0.023    696
  Dihedral  :  3.338  12.856    528
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  6.79 %
    Favored  : 91.18 %
  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 are not related in a simple way.
  whole:  2.98 (0.39), residues: 488
  helix:  2.94 (0.29), residues: 297
  sheet: -0.45 (1.18), residues: 20
  loop :  0.58 (0.51), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 565 
 TYR   0.013   0.001   TYR C 377 
 PHE   0.011   0.001   PHE C 566 
 TRP   0.003   0.001   TRP R  33 
 HIS   0.004   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 4050)
  covalent geometry    : angle       0.42880 ( 5453)
  hydrogen bonds       : bond        0.03546 (  252)
  hydrogen bonds       : angle       3.99072 (  759)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  328 ARG cc_start: 0.4478 (tmt170) cc_final: 0.4251 (ttt180)
REVERT: C  365 MET cc_start: 0.8405 (ttm) cc_final: 0.8031 (tpp)
REVERT: R   25 LYS cc_start: 0.8433 (tttt) cc_final: 0.8002 (tppt)
  outliers start: 9
  outliers final: 8
  residues processed: 41
  average time/residue: 0.1924
  time to fit residues: 9.7725
Evaluate side-chains
  42 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  326 VAL
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  507 MET
Chi-restraints excluded: chain C residue  508 PHE
Chi-restraints excluded: chain C residue  537 ILE
Chi-restraints excluded: chain C residue  597 ASN
Chi-restraints excluded: chain C residue  626 THR
Chi-restraints excluded: chain C residue  711 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 3 optimal weight:    0.1980
   chunk 47 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0980
   chunk 7 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0770
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
C 518 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.089021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.072621 restraints weight = 40617.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.075425 restraints weight = 16524.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.077202 restraints weight = 9321.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.078279 restraints weight = 6468.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.078854 restraints weight = 5188.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4050  Z= 0.100
  Angle     :  0.415   6.183   5453  Z= 0.224
  Chirality :  0.034   0.158    614
  Planarity :  0.002   0.022    696
  Dihedral  :  3.268  12.269    528
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  7.01 %
    Favored  : 91.40 %
  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 are not related in a simple way.
  whole:  3.08 (0.39), residues: 488
  helix:  3.01 (0.29), residues: 297
  sheet: -0.40 (1.18), residues: 20
  loop :  0.64 (0.51), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 573 
 TYR   0.012   0.001   TYR C 377 
 PHE   0.010   0.001   PHE C 566 
 TRP   0.003   0.001   TRP C 581 
 HIS   0.005   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 4050)
  covalent geometry    : angle       0.41460 ( 5453)
  hydrogen bonds       : bond        0.03426 (  252)
  hydrogen bonds       : angle       3.91703 (  759)

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

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

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  976 Ramachandran restraints generated.
    488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  328 ARG cc_start: 0.4494 (tmt170) cc_final: 0.4277 (ttt180)
REVERT: C  365 MET cc_start: 0.8423 (ttm) cc_final: 0.8012 (tpp)
REVERT: C  761 TYR cc_start: 0.7110 (m-80) cc_final: 0.6819 (m-10)
REVERT: R   25 LYS cc_start: 0.8422 (tttt) cc_final: 0.7991 (tppt)
  outliers start: 7
  outliers final: 7
  residues processed: 39
  average time/residue: 0.1605
  time to fit residues: 7.9892
Evaluate side-chains
  42 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  507 MET
Chi-restraints excluded: chain C residue  508 PHE
Chi-restraints excluded: chain C residue  537 ILE
Chi-restraints excluded: chain C residue  597 ASN
Chi-restraints excluded: chain C residue  626 THR
Chi-restraints excluded: chain C residue  711 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0870
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
C 518 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.088451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.072141 restraints weight = 40336.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.074885 restraints weight = 16484.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.076632 restraints weight = 9270.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.077595 restraints weight = 6454.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.078299 restraints weight = 5284.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4050  Z= 0.133
  Angle     :  0.433   5.798   5453  Z= 0.236
  Chirality :  0.034   0.159    614
  Planarity :  0.003   0.036    696
  Dihedral  :  3.309  12.715    528
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  6.79 %
    Favored  : 91.40 %
  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 are not related in a simple way.
  whole:  2.96 (0.39), residues: 488
  helix:  2.94 (0.29), residues: 297
  sheet: -0.47 (1.17), residues: 20
  loop :  0.56 (0.51), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 565 
 TYR   0.014   0.001   TYR C 377 
 PHE   0.011   0.001   PHE C 566 
 TRP   0.003   0.001   TRP R  33 
 HIS   0.006   0.001   HIS C 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4050)
  covalent geometry    : angle       0.43292 ( 5453)
  hydrogen bonds       : bond        0.03530 (  252)
  hydrogen bonds       : angle       3.99000 (  759)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2128.17 seconds
wall clock time: 36 minutes 58.46 seconds (2218.46 seconds total)