Starting phenix.real_space_refine
on Tue Mar  3 12:40:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r0i_53483/03_2026/9r0i_53483.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r0i_53483/03_2026/9r0i_53483.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/9r0i_53483/03_2026/9r0i_53483.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r0i_53483/03_2026/9r0i_53483.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r0i_53483/03_2026/9r0i_53483.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r0i_53483/03_2026/9r0i_53483.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.033
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      35      5.16       5
     Cl      1      4.86       5
     C    2793      2.51       5
     N     693      2.21       5
     O     739      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4261
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 550, 4231
          Classifications: {'peptide': 550}
          Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 517}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'LSN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.20, per 1000 atoms: 0.28
  Number of scatterers: 4261
  At special positions: 0
  Unit cell: (87.36, 93.184, 74.048, 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)
     Cl      1     17.00
     S      35     16.00
     O     739      8.00
     N     693      7.00
     C    2793      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 419 " - pdb=" SG  CYS A 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 444 " - pdb=" SG  CYS A 494 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 450 " - pdb=" SG  CYS A 470 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 492 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 580 " - pdb=" SG  CYS A 594 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 269.9 milliseconds
  

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1020

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 2 sheets defined
      71.3% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 64
      removed outlier: 3.902A  pdb=" N   PHE A  34 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   THR A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   THR A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 91
      removed outlier: 4.138A  pdb=" N   ASN A  77 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   GLU A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ILE A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   PHE A  87 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   PHE A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 94
      No H-bonds generated for 'chain 'A' and resid 92 through 94'
    Processing helix  chain 'A' and resid 96 through 122
      removed outlier: 3.746A  pdb=" N   THR A 116 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
      Proline residue:  A 118  - end of helix
    Processing helix  chain 'A' and resid 168 through 185
      removed outlier: 4.210A  pdb=" N   LEU A 172 " --> pdb=" O   SER A 168 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL A 185 " --> pdb=" O   GLY A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 199
    Processing helix  chain 'A' and resid 203 through 216
      removed outlier: 3.521A  pdb=" N   VAL A 216 " --> pdb=" O   PHE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 230
    Processing helix  chain 'A' and resid 256 through 273
      removed outlier: 3.628A  pdb=" N   GLY A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 277
    Processing helix  chain 'A' and resid 306 through 313
    Processing helix  chain 'A' and resid 313 through 324
    Processing helix  chain 'A' and resid 324 through 357
      removed outlier: 3.631A  pdb=" N   ILE A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR A 346 " --> pdb=" O   ALA A 342 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   ASN A 349 " --> pdb=" O   SER A 345 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   LYS A 350 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLU A 353 " --> pdb=" O   ASN A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 370
    Processing helix  chain 'A' and resid 370 through 389
    Processing helix  chain 'A' and resid 394 through 412
      removed outlier: 4.158A  pdb=" N   ARG A 398 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 416
    Processing helix  chain 'A' and resid 442 through 446
    Processing helix  chain 'A' and resid 468 through 473
    Processing helix  chain 'A' and resid 514 through 531
      removed outlier: 3.536A  pdb=" N   ILE A 531 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 544
      removed outlier: 3.726A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 564
    Processing helix  chain 'A' and resid 567 through 579
      removed outlier: 3.528A  pdb=" N   SER A 579 " --> pdb=" O   LEU A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 635
      removed outlier: 3.601A  pdb=" N   GLN A 610 " --> pdb=" O   TYR A 606 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 466
      removed outlier: 3.510A  pdb=" N   CYS A 459 " --> pdb=" O   LYS A 503 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 488 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   CYS A 492 " --> pdb=" O   CYS A 474 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   CYS A 474 " --> pdb=" O   CYS A 492 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 585
      removed outlier: 5.248A  pdb=" N   CYS A 580 " --> pdb=" O   TYR A 596 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   TYR A 596 " --> pdb=" O   CYS A 580 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   ARG A 582 " --> pdb=" O   CYS A 594 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   CYS A 594 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   ASN A 584 " --> pdb=" O   GLY A 592 " (cutoff:3.500A)

    282 hydrogen bonds defined for protein.
    831 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.52

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1298
        1.34 -     1.46: 1098
        1.46 -     1.58: 1927
        1.58 -     1.70: 0
        1.70 -     1.81: 52
  Bond restraints: 4375
  Sorted by residual:
  bond pdb=" N   SER A  26 "
       pdb=" CA  SER A  26 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.99e+00
  bond pdb=" N   VAL A 464 "
       pdb=" CA  VAL A 464 "
    ideal  model  delta    sigma   weight residual
    1.458  1.479 -0.020 1.21e-02 6.83e+03 2.77e+00
  bond pdb=" N1  LSN A 701 "
       pdb=" N2  LSN A 701 "
    ideal  model  delta    sigma   weight residual
    1.290  1.316 -0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" C   VAL A 464 "
       pdb=" N   GLU A 465 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.43e-02 4.89e+03 1.39e+00
  bond pdb=" N   GLN A 188 "
       pdb=" CA  GLN A 188 "
    ideal  model  delta    sigma   weight residual
    1.462  1.472 -0.010 8.50e-03 1.38e+04 1.39e+00
  ... (remaining 4370 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 5801
        1.21 -     2.42: 102
        2.42 -     3.63: 32
        3.63 -     4.84: 11
        4.84 -     6.04: 1
  Bond angle restraints: 5947
  Sorted by residual:
  angle pdb=" CB  MET A 229 "
        pdb=" CG  MET A 229 "
        pdb=" SD  MET A 229 "
      ideal   model   delta    sigma   weight residual
     112.70  118.74   -6.04 3.00e+00 1.11e-01 4.06e+00
  angle pdb=" C   PHE A 314 "
        pdb=" CA  PHE A 314 "
        pdb=" CB  PHE A 314 "
      ideal   model   delta    sigma   weight residual
     112.76  109.27    3.49 1.86e+00 2.89e-01 3.53e+00
  angle pdb=" N   VAL A 464 "
        pdb=" CA  VAL A 464 "
        pdb=" CB  VAL A 464 "
      ideal   model   delta    sigma   weight residual
     110.56  112.91   -2.35 1.38e+00 5.25e-01 2.90e+00
  angle pdb=" C   GLN A 188 "
        pdb=" CA  GLN A 188 "
        pdb=" CB  GLN A 188 "
      ideal   model   delta    sigma   weight residual
     113.04  110.56    2.48 1.63e+00 3.76e-01 2.32e+00
  angle pdb=" C   VAL A 185 "
        pdb=" CA  VAL A 185 "
        pdb=" CB  VAL A 185 "
      ideal   model   delta    sigma   weight residual
     114.00  112.09    1.91 1.31e+00 5.83e-01 2.13e+00
  ... (remaining 5942 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.86: 2296
       16.86 -    33.72: 216
       33.72 -    50.59: 52
       50.59 -    67.45: 15
       67.45 -    84.31: 9
  Dihedral angle restraints: 2588
    sinusoidal: 999
      harmonic: 1589
  Sorted by residual:
  dihedral pdb=" CB  CYS A 459 "
           pdb=" SG  CYS A 459 "
           pdb=" SG  CYS A 507 "
           pdb=" CB  CYS A 507 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -166.09   80.09     1      1.00e+01 1.00e-02 7.95e+01
  dihedral pdb=" CB  CYS A 450 "
           pdb=" SG  CYS A 450 "
           pdb=" SG  CYS A 470 "
           pdb=" CB  CYS A 470 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -48.16  -37.84     1      1.00e+01 1.00e-02 2.02e+01
  dihedral pdb=" CA  ASP A 235 "
           pdb=" CB  ASP A 235 "
           pdb=" CG  ASP A 235 "
           pdb=" OD1 ASP A 235 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.40   58.40     1      2.00e+01 2.50e-03 1.14e+01
  ... (remaining 2585 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 517
       0.037 -    0.074: 115
       0.074 -    0.111: 41
       0.111 -    0.148: 4
       0.148 -    0.185: 1
  Chirality restraints: 678
  Sorted by residual:
  chirality pdb=" CA  VAL A 464 "
            pdb=" N   VAL A 464 "
            pdb=" C   VAL A 464 "
            pdb=" CB  VAL A 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.57e-01
  chirality pdb=" CA  VAL A 424 "
            pdb=" N   VAL A 424 "
            pdb=" C   VAL A 424 "
            pdb=" CB  VAL A 424 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.63e-01
  chirality pdb=" CA  ILE A 488 "
            pdb=" N   ILE A 488 "
            pdb=" C   ILE A 488 "
            pdb=" CB  ILE A 488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.50e-01
  ... (remaining 675 not shown)

  Planarity restraints: 739
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 LSN A 701 "    0.010 2.00e-02 2.50e+03   1.84e-02 6.76e+00
        pdb=" C11 LSN A 701 "    0.009 2.00e-02 2.50e+03
        pdb=" C12 LSN A 701 "   -0.031 2.00e-02 2.50e+03
        pdb=" C13 LSN A 701 "    0.010 2.00e-02 2.50e+03
        pdb=" C14 LSN A 701 "    0.011 2.00e-02 2.50e+03
        pdb=" C7  LSN A 701 "   -0.033 2.00e-02 2.50e+03
        pdb=" C8  LSN A 701 "    0.011 2.00e-02 2.50e+03
        pdb=" C9  LSN A 701 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 516 "   -0.024 5.00e-02 4.00e+02   3.62e-02 2.09e+00
        pdb=" N   PRO A 517 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 517 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 517 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  LSN A 701 "    0.006 2.00e-02 2.50e+03   9.94e-03 1.98e+00
        pdb=" C2  LSN A 701 "    0.004 2.00e-02 2.50e+03
        pdb=" C3  LSN A 701 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4  LSN A 701 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5  LSN A 701 "    0.000 2.00e-02 2.50e+03
        pdb=" C6  LSN A 701 "    0.011 2.00e-02 2.50e+03
        pdb=" C7  LSN A 701 "    0.013 2.00e-02 2.50e+03
        pdb=" C8  LSN A 701 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 736 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 1484
        2.85 -     3.36: 4285
        3.36 -     3.87: 6824
        3.87 -     4.39: 7743
        4.39 -     4.90: 13556
  Nonbonded interactions: 33892
  Sorted by model distance:
  nonbonded pdb=" O   ILE A  85 "
            pdb=" OG  SER A  89 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" O   SER A  55 "
            pdb=" OG  SER A  55 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" N   ASP A 547 "
            pdb=" OD1 ASP A 547 "
     model   vdw
     2.380 3.120
  nonbonded pdb=" N   SER A 247 "
            pdb=" OD2 ASP A 250 "
     model   vdw
     2.409 3.120
  nonbonded pdb=" O   ILE A 519 "
            pdb=" OG  SER A 523 "
     model   vdw
     2.440 3.040
  ... (remaining 33887 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.310
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
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   0.033   4381  Z= 0.140
  Angle     :  0.481   6.044   5959  Z= 0.241
  Chirality :  0.037   0.185    678
  Planarity :  0.004   0.036    739
  Dihedral  : 14.979  84.309   1550
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 13.49 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  2.83 (0.37), residues: 544
  helix:  2.67 (0.28), residues: 341
  sheet:  None (None), residues: 0
  loop :  0.57 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  99 
 TYR   0.008   0.001   TYR A 236 
 PHE   0.015   0.001   PHE A 557 
 TRP   0.006   0.001   TRP A 565 
 HIS   0.001   0.000   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4375)
  covalent geometry    : angle       0.48102 ( 5947)
  SS BOND              : bond        0.00124 (    6)
  SS BOND              : angle       0.38151 (   12)
  hydrogen bonds       : bond        0.20344 (  282)
  hydrogen bonds       : angle       6.85386 (  831)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  170 TRP cc_start: 0.8000 (t60) cc_final: 0.7754 (t60)
REVERT: A  465 GLU cc_start: 0.8451 (tt0) cc_final: 0.7668 (tt0)
  outliers start: 1
  outliers final: 1
  residues processed: 89
  average time/residue: 0.0611
  time to fit residues: 7.0962
Evaluate side-chains
  59 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.1980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 491 ASN
A 534 ASN
A 556 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.115514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.082822 restraints weight = 7974.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.97
r_work: 0.3000 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4381  Z= 0.141
  Angle     :  0.552   6.176   5959  Z= 0.279
  Chirality :  0.041   0.170    678
  Planarity :  0.005   0.037    739
  Dihedral  :  4.998  57.365    609
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.49 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.16 (0.36), residues: 544
  helix:  2.82 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop :  0.75 (0.46), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  99 
 TYR   0.016   0.001   TYR A  90 
 PHE   0.016   0.001   PHE A 455 
 TRP   0.013   0.001   TRP A 565 
 HIS   0.002   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4375)
  covalent geometry    : angle       0.55231 ( 5947)
  SS BOND              : bond        0.00196 (    6)
  SS BOND              : angle       0.62432 (   12)
  hydrogen bonds       : bond        0.04879 (  282)
  hydrogen bonds       : angle       4.50723 (  831)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  170 TRP cc_start: 0.7787 (t60) cc_final: 0.7535 (t60)
REVERT: A  465 GLU cc_start: 0.8866 (tt0) cc_final: 0.7946 (tt0)
  outliers start: 10
  outliers final: 5
  residues processed: 74
  average time/residue: 0.0621
  time to fit residues: 6.0984
Evaluate side-chains
  61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  562 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0040
   chunk 16 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 41 optimal weight:    0.3980
   chunk 8 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.4592

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.116838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.083792 restraints weight = 7931.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 3.00
r_work: 0.3028 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4381  Z= 0.118
  Angle     :  0.518   6.690   5959  Z= 0.257
  Chirality :  0.040   0.153    678
  Planarity :  0.004   0.036    739
  Dihedral  :  4.699  51.335    609
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.56 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.15 (0.36), residues: 544
  helix:  2.88 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop :  0.60 (0.45), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  99 
 TYR   0.018   0.001   TYR A 489 
 PHE   0.011   0.001   PHE A 347 
 TRP   0.010   0.001   TRP A 565 
 HIS   0.002   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4375)
  covalent geometry    : angle       0.51626 ( 5947)
  SS BOND              : bond        0.00483 (    6)
  SS BOND              : angle       1.11002 (   12)
  hydrogen bonds       : bond        0.03966 (  282)
  hydrogen bonds       : angle       4.09662 (  831)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  170 TRP cc_start: 0.7722 (t60) cc_final: 0.7502 (t60)
REVERT: A  323 MET cc_start: 0.7921 (mmp) cc_final: 0.7626 (mmm)
REVERT: A  379 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7869 (mmt)
REVERT: A  465 GLU cc_start: 0.8731 (tt0) cc_final: 0.7956 (tt0)
  outliers start: 13
  outliers final: 6
  residues processed: 70
  average time/residue: 0.0511
  time to fit residues: 4.8820
Evaluate side-chains
  59 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  407 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 41 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0980
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.117175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.084726 restraints weight = 7867.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 3.07
r_work: 0.3026 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4381  Z= 0.112
  Angle     :  0.505   7.505   5959  Z= 0.251
  Chirality :  0.039   0.144    678
  Planarity :  0.004   0.034    739
  Dihedral  :  4.434  48.281    609
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.99 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.25 (0.36), residues: 544
  helix:  2.94 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop :  0.64 (0.46), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  99 
 TYR   0.011   0.001   TYR A  90 
 PHE   0.010   0.001   PHE A 198 
 TRP   0.008   0.001   TRP A 565 
 HIS   0.002   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 4375)
  covalent geometry    : angle       0.50458 ( 5947)
  SS BOND              : bond        0.00324 (    6)
  SS BOND              : angle       0.80933 (   12)
  hydrogen bonds       : bond        0.03624 (  282)
  hydrogen bonds       : angle       3.94417 (  831)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  170 TRP cc_start: 0.7730 (t60) cc_final: 0.7504 (t60)
REVERT: A  323 MET cc_start: 0.7946 (mmp) cc_final: 0.7660 (mmm)
REVERT: A  379 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7819 (mmt)
REVERT: A  411 CYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8465 (t)
REVERT: A  465 GLU cc_start: 0.8720 (tt0) cc_final: 0.7953 (tt0)
  outliers start: 12
  outliers final: 4
  residues processed: 68
  average time/residue: 0.0590
  time to fit residues: 5.3479
Evaluate side-chains
  58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  411 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 48 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.115652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.083157 restraints weight = 7929.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 3.05
r_work: 0.3007 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4381  Z= 0.136
  Angle     :  0.518   7.204   5959  Z= 0.255
  Chirality :  0.040   0.137    678
  Planarity :  0.004   0.032    739
  Dihedral  :  4.380  47.467    609
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.70 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.28 (0.36), residues: 544
  helix:  2.93 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop :  0.74 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  99 
 TYR   0.009   0.001   TYR A  90 
 PHE   0.009   0.001   PHE A 198 
 TRP   0.008   0.001   TRP A 170 
 HIS   0.002   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4375)
  covalent geometry    : angle       0.51814 ( 5947)
  SS BOND              : bond        0.00275 (    6)
  SS BOND              : angle       0.66484 (   12)
  hydrogen bonds       : bond        0.03704 (  282)
  hydrogen bonds       : angle       3.92615 (  831)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  170 TRP cc_start: 0.7742 (t60) cc_final: 0.7540 (t60)
REVERT: A  323 MET cc_start: 0.7977 (mmp) cc_final: 0.7692 (mmm)
REVERT: A  379 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7871 (mmt)
REVERT: A  411 CYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8496 (t)
REVERT: A  465 GLU cc_start: 0.8683 (tt0) cc_final: 0.7936 (tt0)
  outliers start: 11
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0597
  time to fit residues: 5.0113
Evaluate side-chains
  60 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  411 CYS
Chi-restraints excluded: chain A residue  562 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0370
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0670
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.116689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.084352 restraints weight = 8084.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 3.09
r_work: 0.3026 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4381  Z= 0.113
  Angle     :  0.498   6.306   5959  Z= 0.244
  Chirality :  0.039   0.135    678
  Planarity :  0.004   0.033    739
  Dihedral  :  4.278  47.940    609
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.70 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.31 (0.36), residues: 544
  helix:  2.98 (0.27), residues: 356
  sheet:  None (None), residues: 0
  loop :  0.69 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 238 
 TYR   0.009   0.001   TYR A  90 
 PHE   0.010   0.001   PHE A 337 
 TRP   0.009   0.001   TRP A 170 
 HIS   0.002   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4375)
  covalent geometry    : angle       0.49819 ( 5947)
  SS BOND              : bond        0.00213 (    6)
  SS BOND              : angle       0.59413 (   12)
  hydrogen bonds       : bond        0.03388 (  282)
  hydrogen bonds       : angle       3.81231 (  831)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  323 MET cc_start: 0.7934 (mmp) cc_final: 0.7656 (mmm)
REVERT: A  411 CYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8450 (t)
REVERT: A  465 GLU cc_start: 0.8647 (tt0) cc_final: 0.7925 (tt0)
REVERT: A  537 TYR cc_start: 0.8892 (t80) cc_final: 0.8454 (t80)
  outliers start: 10
  outliers final: 5
  residues processed: 67
  average time/residue: 0.0594
  time to fit residues: 5.3607
Evaluate side-chains
  60 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  411 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 35 optimal weight:    0.0370
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0670
   chunk 43 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0970
   chunk 16 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.2994

-------------------------------------------------------------------------------
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 = 0.3703 r_free = 0.3703 target = 0.117570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.085368 restraints weight = 8057.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.10
r_work: 0.3044 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4381  Z= 0.103
  Angle     :  0.516   7.129   5959  Z= 0.249
  Chirality :  0.039   0.124    678
  Planarity :  0.004   0.033    739
  Dihedral  :  4.250  49.027    609
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.70 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.39 (0.37), residues: 544
  helix:  3.05 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop :  0.75 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 238 
 TYR   0.008   0.001   TYR A  90 
 PHE   0.008   0.001   PHE A 337 
 TRP   0.009   0.001   TRP A 565 
 HIS   0.002   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 4375)
  covalent geometry    : angle       0.51611 ( 5947)
  SS BOND              : bond        0.00178 (    6)
  SS BOND              : angle       0.46967 (   12)
  hydrogen bonds       : bond        0.03201 (  282)
  hydrogen bonds       : angle       3.78542 (  831)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  323 MET cc_start: 0.7937 (mmp) cc_final: 0.7656 (mmm)
REVERT: A  379 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7864 (mmt)
REVERT: A  465 GLU cc_start: 0.8596 (tt0) cc_final: 0.7932 (tt0)
REVERT: A  537 TYR cc_start: 0.8849 (t80) cc_final: 0.8472 (t80)
  outliers start: 9
  outliers final: 4
  residues processed: 65
  average time/residue: 0.0604
  time to fit residues: 5.2603
Evaluate side-chains
  61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  459 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3676 r_free = 0.3676 target = 0.115565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.083249 restraints weight = 8061.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 3.09
r_work: 0.3011 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4381  Z= 0.134
  Angle     :  0.530   7.767   5959  Z= 0.255
  Chirality :  0.040   0.123    678
  Planarity :  0.004   0.030    739
  Dihedral  :  3.985  49.521    607
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.34 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.38 (0.37), residues: 544
  helix:  3.01 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop :  0.82 (0.48), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 627 
 TYR   0.007   0.001   TYR A 194 
 PHE   0.011   0.001   PHE A 337 
 TRP   0.008   0.001   TRP A 565 
 HIS   0.002   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4375)
  covalent geometry    : angle       0.53040 ( 5947)
  SS BOND              : bond        0.00150 (    6)
  SS BOND              : angle       0.55944 (   12)
  hydrogen bonds       : bond        0.03505 (  282)
  hydrogen bonds       : angle       3.83794 (  831)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  323 MET cc_start: 0.7987 (mmp) cc_final: 0.7710 (mmm)
REVERT: A  379 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7911 (mmt)
REVERT: A  465 GLU cc_start: 0.8625 (tt0) cc_final: 0.7969 (tt0)
REVERT: A  537 TYR cc_start: 0.8860 (t80) cc_final: 0.8557 (t80)
  outliers start: 8
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0609
  time to fit residues: 4.9200
Evaluate side-chains
  61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  459 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 41 optimal weight:    0.0770
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 34 optimal weight:    0.2980
   chunk 33 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0980
   overall best weight:    0.4338

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.116884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.084805 restraints weight = 8062.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 3.08
r_work: 0.3036 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4381  Z= 0.109
  Angle     :  0.540   8.059   5959  Z= 0.260
  Chirality :  0.039   0.124    678
  Planarity :  0.004   0.031    739
  Dihedral  :  4.091  49.287    607
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.92 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.35 (0.37), residues: 544
  helix:  3.02 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop :  0.72 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 238 
 TYR   0.007   0.001   TYR A  90 
 PHE   0.008   0.001   PHE A 347 
 TRP   0.009   0.001   TRP A 565 
 HIS   0.001   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4375)
  covalent geometry    : angle       0.53449 ( 5947)
  SS BOND              : bond        0.00244 (    6)
  SS BOND              : angle       1.74339 (   12)
  hydrogen bonds       : bond        0.03285 (  282)
  hydrogen bonds       : angle       3.77583 (  831)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  323 MET cc_start: 0.7939 (mmp) cc_final: 0.7661 (mmm)
REVERT: A  379 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7996 (mmt)
REVERT: A  465 GLU cc_start: 0.8459 (tt0) cc_final: 0.7921 (tt0)
REVERT: A  537 TYR cc_start: 0.8828 (t80) cc_final: 0.8482 (t80)
  outliers start: 9
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0575
  time to fit residues: 4.9585
Evaluate side-chains
  64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  459 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 51 optimal weight:    0.1980
   chunk 48 optimal weight:    0.0570
   chunk 19 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    0.4898

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.116791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.084527 restraints weight = 8114.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 3.11
r_work: 0.3037 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4381  Z= 0.111
  Angle     :  0.540   8.512   5959  Z= 0.259
  Chirality :  0.039   0.131    678
  Planarity :  0.004   0.032    739
  Dihedral  :  4.076  49.626    607
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.34 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.38 (0.37), residues: 544
  helix:  3.04 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop :  0.75 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  99 
 TYR   0.008   0.001   TYR A  90 
 PHE   0.008   0.001   PHE A 337 
 TRP   0.009   0.001   TRP A 565 
 HIS   0.001   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4375)
  covalent geometry    : angle       0.53541 ( 5947)
  SS BOND              : bond        0.00298 (    6)
  SS BOND              : angle       1.60104 (   12)
  hydrogen bonds       : bond        0.03244 (  282)
  hydrogen bonds       : angle       3.74928 (  831)

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

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

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1088 Ramachandran restraints generated.
    544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  323 MET cc_start: 0.7950 (mmp) cc_final: 0.7672 (mmm)
REVERT: A  379 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8018 (mmt)
REVERT: A  465 GLU cc_start: 0.8500 (tt0) cc_final: 0.7916 (tt0)
REVERT: A  537 TYR cc_start: 0.8844 (t80) cc_final: 0.8501 (t80)
  outliers start: 8
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0612
  time to fit residues: 5.2349
Evaluate side-chains
  64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  459 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0980
   chunk 11 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0980
   chunk 44 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.116707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.084361 restraints weight = 7985.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 3.09
r_work: 0.3034 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4381  Z= 0.115
  Angle     :  0.540   8.489   5959  Z= 0.258
  Chirality :  0.039   0.122    678
  Planarity :  0.004   0.032    739
  Dihedral  :  4.071  49.667    607
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.77 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  3.39 (0.36), residues: 544
  helix:  3.04 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop :  0.76 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  99 
 TYR   0.007   0.001   TYR A  90 
 PHE   0.009   0.001   PHE A 337 
 TRP   0.008   0.001   TRP A 565 
 HIS   0.001   0.000   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4375)
  covalent geometry    : angle       0.53650 ( 5947)
  SS BOND              : bond        0.00226 (    6)
  SS BOND              : angle       1.40141 (   12)
  hydrogen bonds       : bond        0.03285 (  282)
  hydrogen bonds       : angle       3.75251 (  831)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1208.98 seconds
wall clock time: 21 minutes 20.66 seconds (1280.66 seconds total)