Starting phenix.real_space_refine
on Tue Aug  4 20:22:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jxp_61871/08_2026/9jxp_61871.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jxp_61871/08_2026/9jxp_61871.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jxp_61871/08_2026/9jxp_61871.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jxp_61871/08_2026/9jxp_61871.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jxp_61871/08_2026/9jxp_61871.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jxp_61871/08_2026/9jxp_61871.cif"
  }
  resolution = 3.53
  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=   0.004 sd=   0.091
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4326      2.51       5
     N    1024      2.21       5
     O    1048      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6430
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 3215
          Classifications: {'peptide': 385}
          Link IDs: {'PTRANS': 12, 'TRANS': 372}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.87, per 1000 atoms: 0.29
  Number of scatterers: 6430
  At special positions: 0
  Unit cell: (119.215, 66.465, 75.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1048      8.00
     N    1024      7.00
     C    4326      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " 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: 0.45
  Conformation dependent library (CDL) restraints added in 363.9 milliseconds
  

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1464

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      77.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 231 through 258
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 4.371A  pdb=" N   ILE A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 4.364A  pdb=" N   ILE A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 336
      removed outlier: 3.790A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 361
      removed outlier: 4.184A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A 359 " --> pdb=" O   MET A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 384 through 387
    Processing helix  chain 'A' and resid 390 through 403
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.913A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 470
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 473 through 503
      removed outlier: 3.636A  pdb=" N   LEU A 477 " --> pdb=" O   ALA A 473 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL A 478 " --> pdb=" O   PHE A 474 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   ASN A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS A 482 " --> pdb=" O   VAL A 478 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   TYR A 483 " --> pdb=" O   ASN A 479 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 3.622A  pdb=" N   PHE A 510 " --> pdb=" O   ASP A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 570
      removed outlier: 3.818A  pdb=" N   TYR A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 570 " --> pdb=" O   ASP A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 581
      removed outlier: 3.558A  pdb=" N   GLN A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 619
      Proline residue:  A 598  - end of helix
      removed outlier: 4.487A  pdb=" N   GLU A 613 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 258
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 4.371A  pdb=" N   ILE B 271 " --> pdb=" O   PRO B 267 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 4.364A  pdb=" N   ILE B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 336
      removed outlier: 3.791A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 361
      removed outlier: 4.185A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU B 359 " --> pdb=" O   MET B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'B' and resid 384 through 387
    Processing helix  chain 'B' and resid 390 through 403
    Processing helix  chain 'B' and resid 403 through 419
      removed outlier: 3.913A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 470
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 473 through 503
      removed outlier: 3.636A  pdb=" N   LEU B 477 " --> pdb=" O   ALA B 473 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL B 478 " --> pdb=" O   PHE B 474 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   ASN B 479 " --> pdb=" O   PRO B 475 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS B 482 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   TYR B 483 " --> pdb=" O   ASN B 479 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.622A  pdb=" N   PHE B 510 " --> pdb=" O   ASP B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 570
      removed outlier: 3.818A  pdb=" N   TYR B 560 " --> pdb=" O   LYS B 556 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU B 570 " --> pdb=" O   ASP B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 581
      removed outlier: 3.558A  pdb=" N   GLN B 576 " --> pdb=" O   ALA B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 619
      Proline residue:  B 598  - end of helix
      removed outlier: 4.486A  pdb=" N   GLU B 613 " --> pdb=" O   PHE B 609 " (cutoff:3.500A)

    432 hydrogen bonds defined for protein.
    1290 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: 0.70

  Time building geometry restraints manager: 0.64 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: 1888
        1.34 -     1.46: 1801
        1.46 -     1.58: 2913
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 6646
  Sorted by residual:
  bond pdb=" C   GLY B 621 "
       pdb=" N   GLU B 622 "
    ideal  model  delta    sigma   weight residual
    1.334  1.303  0.031 1.25e-02 6.40e+03 5.96e+00
  bond pdb=" C   GLY A 621 "
       pdb=" N   GLU A 622 "
    ideal  model  delta    sigma   weight residual
    1.334  1.305  0.029 1.25e-02 6.40e+03 5.55e+00
  bond pdb=" CB  VAL B 246 "
       pdb=" CG1 VAL B 246 "
    ideal  model  delta    sigma   weight residual
    1.521  1.457  0.064 3.30e-02 9.18e+02 3.76e+00
  bond pdb=" CB  VAL A 246 "
       pdb=" CG1 VAL A 246 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.65e+00
  bond pdb=" CA  GLU B 622 "
       pdb=" C   GLU B 622 "
    ideal  model  delta    sigma   weight residual
    1.530  1.518  0.011 1.10e-02 8.26e+03 1.06e+00
  ... (remaining 6641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 8634
        1.52 -     3.03: 332
        3.03 -     4.55: 52
        4.55 -     6.07: 18
        6.07 -     7.58: 6
  Bond angle restraints: 9042
  Sorted by residual:
  angle pdb=" N   GLU A 622 "
        pdb=" CA  GLU A 622 "
        pdb=" CB  GLU A 622 "
      ideal   model   delta    sigma   weight residual
     110.60  104.20    6.40 1.51e+00 4.39e-01 1.80e+01
  angle pdb=" N   GLU B 622 "
        pdb=" CA  GLU B 622 "
        pdb=" CB  GLU B 622 "
      ideal   model   delta    sigma   weight residual
     110.60  104.25    6.35 1.51e+00 4.39e-01 1.77e+01
  angle pdb=" CA  GLU B 622 "
        pdb=" C   GLU B 622 "
        pdb=" O   GLU B 622 "
      ideal   model   delta    sigma   weight residual
     122.64  117.85    4.79 1.25e+00 6.40e-01 1.47e+01
  angle pdb=" CA  GLU A 622 "
        pdb=" C   GLU A 622 "
        pdb=" O   GLU A 622 "
      ideal   model   delta    sigma   weight residual
     122.64  117.93    4.71 1.25e+00 6.40e-01 1.42e+01
  angle pdb=" N   HIS A 441 "
        pdb=" CA  HIS A 441 "
        pdb=" C   HIS A 441 "
      ideal   model   delta    sigma   weight residual
     113.28  108.74    4.54 1.57e+00 4.06e-01 8.36e+00
  ... (remaining 9037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 3363
       17.89 -    35.79: 314
       35.79 -    53.68: 69
       53.68 -    71.57: 4
       71.57 -    89.47: 4
  Dihedral angle restraints: 3754
    sinusoidal: 1482
      harmonic: 2272
  Sorted by residual:
  dihedral pdb=" CA  LEU B 569 "
           pdb=" C   LEU B 569 "
           pdb=" N   LEU B 570 "
           pdb=" CA  LEU B 570 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.46   20.54     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  LEU A 569 "
           pdb=" C   LEU A 569 "
           pdb=" N   LEU A 570 "
           pdb=" CA  LEU A 570 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.55   20.45     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  CYS B 440 "
           pdb=" C   CYS B 440 "
           pdb=" N   HIS B 441 "
           pdb=" CA  HIS B 441 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.69  -18.31     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 3751 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 528
       0.029 -    0.058: 307
       0.058 -    0.087: 117
       0.087 -    0.116: 34
       0.116 -    0.145: 4
  Chirality restraints: 990
  Sorted by residual:
  chirality pdb=" CB  ILE A 360 "
            pdb=" CA  ILE A 360 "
            pdb=" CG1 ILE A 360 "
            pdb=" CG2 ILE A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CB  ILE B 360 "
            pdb=" CA  ILE B 360 "
            pdb=" CG1 ILE B 360 "
            pdb=" CG2 ILE B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.14 2.00e-01 2.50e+01 4.99e-01
  chirality pdb=" CA  GLU A 622 "
            pdb=" N   GLU A 622 "
            pdb=" C   GLU A 622 "
            pdb=" CB  GLU A 622 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.61e-01
  ... (remaining 987 not shown)

  Planarity restraints: 1096
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 609 "   -0.018 2.00e-02 2.50e+03   1.48e-02 3.81e+00
        pdb=" CG  PHE B 609 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 609 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 609 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 609 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 609 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 609 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 609 "   -0.018 2.00e-02 2.50e+03   1.46e-02 3.73e+00
        pdb=" CG  PHE A 609 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 609 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 609 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 609 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 609 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 609 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 337 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO A 338 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 338 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 338 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1093 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 70
        2.65 -     3.21: 6366
        3.21 -     3.78: 10252
        3.78 -     4.34: 13112
        4.34 -     4.90: 21682
  Nonbonded interactions: 51482
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 318 "
            pdb=" OH  TYR B 367 "
     model   vdw
     2.088 3.040
  nonbonded pdb=" OE2 GLU A 318 "
            pdb=" OH  TYR A 367 "
     model   vdw
     2.088 3.040
  nonbonded pdb=" OH  TYR B 272 "
            pdb=" OG  SER B 330 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OH  TYR A 272 "
            pdb=" OG  SER A 330 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" NH1 ARG A 270 "
            pdb=" OD1 ASP A 590 "
     model   vdw
     2.281 3.120
  ... (remaining 51477 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.360
  Find NCS groups from input model:        0.060
  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:   10.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
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      :  0.005   0.064   6648  Z= 0.228
  Angle     :  0.715   7.584   9046  Z= 0.415
  Chirality :  0.041   0.145    990
  Planarity :  0.004   0.046   1096
  Dihedral  : 14.250  89.465   2284
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  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: -2.60 (0.27), residues: 762
  helix: -0.76 (0.19), residues: 552
  sheet:  None (None), residues: 0
  loop : -4.25 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 611 
 TYR   0.026   0.002   TYR B 518 
 PHE   0.034   0.002   PHE B 609 
 TRP   0.006   0.001   TRP A 457 
 HIS   0.010   0.002   HIS A 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00515 /  0.23 ( 6646)
  covalent geometry    : angle       0.71401 /  0.42 ( 9042)
  SS BOND              : bond        0.00230 /  0.16 (    2)
  SS BOND              : angle       1.72681 /  0.97 (    4)
  hydrogen bonds       : bond        0.10453 /  6.35 (  432)
  hydrogen bonds       : angle       5.41007 /  4.03 ( 1290)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  445 TYR cc_start: 0.8013 (m-80) cc_final: 0.7768 (m-80)
REVERT: A  468 ARG cc_start: 0.7488 (ttp80) cc_final: 0.6609 (ttm170)
REVERT: A  565 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: A  579 ILE cc_start: 0.8612 (tp) cc_final: 0.8296 (tp)
REVERT: A  615 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7515 (tp30)
REVERT: B  445 TYR cc_start: 0.8012 (m-80) cc_final: 0.7748 (m-80)
REVERT: B  468 ARG cc_start: 0.7446 (ttp80) cc_final: 0.6544 (ttm170)
REVERT: B  508 MET cc_start: 0.7993 (tpt) cc_final: 0.7710 (tpp)
REVERT: B  565 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8231 (tm-30)
REVERT: B  579 ILE cc_start: 0.8584 (tp) cc_final: 0.8264 (tp)
REVERT: B  615 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7451 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0579
  time to fit residues: 9.0006
Evaluate side-chains
  87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.0060
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 452 GLN
A 476 HIS
A 618 ASN
A 619 ASN
B 452 GLN
B 476 HIS
B 618 ASN
B 619 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.166443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.120864 restraints weight = 6953.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.125005 restraints weight = 4350.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.127748 restraints weight = 3319.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.129350 restraints weight = 2831.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.130508 restraints weight = 2572.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6648  Z= 0.152
  Angle     :  0.602   8.928   9046  Z= 0.310
  Chirality :  0.039   0.131    990
  Planarity :  0.004   0.043   1096
  Dihedral  :  4.274  18.202    848
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.08 %
    Favored  : 82.31 %
  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: -0.87 (0.31), residues: 762
  helix:  0.57 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -3.83 (0.41), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 472 
 TYR   0.017   0.001   TYR A 518 
 PHE   0.012   0.001   PHE B 609 
 TRP   0.005   0.001   TRP A 266 
 HIS   0.008   0.001   HIS B 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.15 ( 6646)
  covalent geometry    : angle       0.60173 /  0.31 ( 9042)
  SS BOND              : bond        0.00022 /  0.01 (    2)
  SS BOND              : angle       1.34487 /  0.83 (    4)
  hydrogen bonds       : bond        0.04398 /  2.92 (  432)
  hydrogen bonds       : angle       4.32531 /  3.23 ( 1290)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  270 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7821 (mtm-85)
REVERT: A  445 TYR cc_start: 0.8320 (m-80) cc_final: 0.7969 (m-80)
REVERT: A  468 ARG cc_start: 0.7423 (ttp80) cc_final: 0.6403 (ttm170)
REVERT: A  487 PHE cc_start: 0.7031 (m-10) cc_final: 0.6668 (m-10)
REVERT: A  550 GLU cc_start: 0.8229 (pm20) cc_final: 0.7790 (pm20)
REVERT: A  565 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7807 (tm-30)
REVERT: A  579 ILE cc_start: 0.8222 (tp) cc_final: 0.7922 (tp)
REVERT: A  615 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7203 (tp30)
REVERT: B  270 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7803 (mtm-85)
REVERT: B  445 TYR cc_start: 0.8316 (m-80) cc_final: 0.7961 (m-80)
REVERT: B  468 ARG cc_start: 0.7389 (ttp80) cc_final: 0.6364 (ttm170)
REVERT: B  487 PHE cc_start: 0.6898 (m-10) cc_final: 0.6534 (m-10)
REVERT: B  508 MET cc_start: 0.7864 (tpt) cc_final: 0.7642 (tpp)
REVERT: B  550 GLU cc_start: 0.8230 (pm20) cc_final: 0.7752 (pm20)
REVERT: B  565 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7719 (tm-30)
REVERT: B  579 ILE cc_start: 0.8233 (tp) cc_final: 0.7922 (tp)
REVERT: B  615 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7149 (tp30)
  outliers start: 11
  outliers final: 7
  residues processed: 100
  average time/residue: 0.0712
  time to fit residues: 9.7295
Evaluate side-chains
  93 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain B residue  612 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0970
   overall best weight:    0.6378

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.166528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.121239 restraints weight = 6884.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.125326 restraints weight = 4328.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.127991 restraints weight = 3312.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.129563 restraints weight = 2815.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.130804 restraints weight = 2555.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6648  Z= 0.149
  Angle     :  0.575   7.561   9046  Z= 0.297
  Chirality :  0.038   0.135    990
  Planarity :  0.004   0.042   1096
  Dihedral  :  4.061  16.779    848
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 18.57 %
    Favored  : 78.07 %
  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: -0.03 (0.32), residues: 762
  helix:  1.19 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -3.50 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 472 
 TYR   0.014   0.001   TYR B 518 
 PHE   0.016   0.001   PHE B 609 
 TRP   0.005   0.001   TRP A 457 
 HIS   0.007   0.001   HIS B 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 6646)
  covalent geometry    : angle       0.57391 /  0.30 ( 9042)
  SS BOND              : bond        0.00070 /  0.05 (    2)
  SS BOND              : angle       1.41763 /  0.89 (    4)
  hydrogen bonds       : bond        0.04284 /  2.85 (  432)
  hydrogen bonds       : angle       4.05799 /  3.04 ( 1290)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  270 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7899 (mtm-85)
REVERT: A  445 TYR cc_start: 0.8256 (m-80) cc_final: 0.7902 (m-80)
REVERT: A  468 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6363 (ttm170)
REVERT: A  487 PHE cc_start: 0.7097 (m-10) cc_final: 0.6652 (m-10)
REVERT: A  550 GLU cc_start: 0.8265 (pm20) cc_final: 0.7904 (pm20)
REVERT: A  565 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7749 (tm-30)
REVERT: A  579 ILE cc_start: 0.8083 (tp) cc_final: 0.7827 (tp)
REVERT: A  609 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6926 (t80)
REVERT: A  615 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7223 (tp30)
REVERT: B  270 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7760 (mtm-85)
REVERT: B  445 TYR cc_start: 0.8237 (m-80) cc_final: 0.7883 (m-80)
REVERT: B  468 ARG cc_start: 0.7357 (ttp80) cc_final: 0.6298 (ttm170)
REVERT: B  508 MET cc_start: 0.7881 (tpt) cc_final: 0.7672 (tpp)
REVERT: B  550 GLU cc_start: 0.8248 (pm20) cc_final: 0.7886 (pm20)
REVERT: B  565 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7559 (tm-30)
REVERT: B  579 ILE cc_start: 0.8053 (tp) cc_final: 0.7800 (tp)
REVERT: B  609 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6896 (t80)
REVERT: B  615 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7471 (tp30)
  outliers start: 23
  outliers final: 17
  residues processed: 97
  average time/residue: 0.0720
  time to fit residues: 9.5507
Evaluate side-chains
  102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  609 PHE
Chi-restraints excluded: chain B residue  612 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0470
   chunk 50 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 45 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.7434 > 50:)
   chunk 15 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.5878

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 441 HIS
** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.167101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.122324 restraints weight = 6880.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.126399 restraints weight = 4304.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.129255 restraints weight = 3268.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.130606 restraints weight = 2777.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.131862 restraints weight = 2539.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6648  Z= 0.141
  Angle     :  0.569   9.113   9046  Z= 0.289
  Chirality :  0.038   0.132    990
  Planarity :  0.004   0.040   1096
  Dihedral  :  3.937  15.995    848
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 21.20 %
    Favored  : 75.00 %
  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:  0.43 (0.32), residues: 762
  helix:  1.53 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -3.34 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 611 
 TYR   0.011   0.001   TYR A 553 
 PHE   0.013   0.001   PHE B 609 
 TRP   0.006   0.001   TRP B 573 
 HIS   0.005   0.001   HIS B 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 ( 6646)
  covalent geometry    : angle       0.56876 /  0.29 ( 9042)
  SS BOND              : bond        0.00077 /  0.05 (    2)
  SS BOND              : angle       1.23216 /  0.77 (    4)
  hydrogen bonds       : bond        0.04143 /  2.76 (  432)
  hydrogen bonds       : angle       3.90145 /  2.92 ( 1290)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  372 PHE cc_start: 0.7827 (m-10) cc_final: 0.7563 (m-80)
REVERT: A  445 TYR cc_start: 0.8158 (m-80) cc_final: 0.7820 (m-80)
REVERT: A  468 ARG cc_start: 0.7371 (ttp80) cc_final: 0.6370 (ttm170)
REVERT: A  487 PHE cc_start: 0.7120 (m-10) cc_final: 0.6671 (m-10)
REVERT: A  550 GLU cc_start: 0.8175 (pm20) cc_final: 0.7801 (pm20)
REVERT: A  565 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: A  579 ILE cc_start: 0.8128 (tp) cc_final: 0.7876 (tp)
REVERT: A  609 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6764 (t80)
REVERT: A  615 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7272 (tp30)
REVERT: B  270 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7785 (mtm-85)
REVERT: B  445 TYR cc_start: 0.8143 (m-80) cc_final: 0.7814 (m-80)
REVERT: B  550 GLU cc_start: 0.8161 (pm20) cc_final: 0.7822 (pm20)
REVERT: B  565 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7541 (tm-30)
REVERT: B  579 ILE cc_start: 0.8168 (tp) cc_final: 0.7908 (tp)
REVERT: B  609 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6779 (t80)
REVERT: B  615 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7529 (tp30)
  outliers start: 26
  outliers final: 18
  residues processed: 100
  average time/residue: 0.0790
  time to fit residues: 10.6807
Evaluate side-chains
  97 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  441 HIS
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  609 PHE
Chi-restraints excluded: chain B residue  612 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0970
   chunk 32 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.6578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.165838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.121721 restraints weight = 6939.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.125784 restraints weight = 4333.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.128308 restraints weight = 3292.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.130236 restraints weight = 2796.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131238 restraints weight = 2517.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6648  Z= 0.148
  Angle     :  0.567   7.309   9046  Z= 0.291
  Chirality :  0.038   0.140    990
  Planarity :  0.004   0.040   1096
  Dihedral  :  3.933  15.987    848
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 21.35 %
    Favored  : 74.27 %
  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:  0.60 (0.32), residues: 762
  helix:  1.61 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -3.19 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 270 
 TYR   0.012   0.001   TYR B 553 
 PHE   0.015   0.001   PHE A 609 
 TRP   0.007   0.001   TRP B 573 
 HIS   0.005   0.001   HIS B 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 6646)
  covalent geometry    : angle       0.56681 /  0.29 ( 9042)
  SS BOND              : bond        0.00023 /  0.02 (    2)
  SS BOND              : angle       1.08065 /  0.71 (    4)
  hydrogen bonds       : bond        0.04187 /  2.79 (  432)
  hydrogen bonds       : angle       3.86663 /  2.90 ( 1290)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  372 PHE cc_start: 0.7804 (m-10) cc_final: 0.7502 (m-80)
REVERT: A  468 ARG cc_start: 0.7385 (ttp80) cc_final: 0.6390 (ttm170)
REVERT: A  550 GLU cc_start: 0.8180 (pm20) cc_final: 0.7803 (pm20)
REVERT: A  565 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: A  579 ILE cc_start: 0.8228 (tp) cc_final: 0.7985 (tp)
REVERT: A  609 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6825 (t80)
REVERT: A  615 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7298 (tp30)
REVERT: B  372 PHE cc_start: 0.7842 (m-10) cc_final: 0.7551 (m-80)
REVERT: B  487 PHE cc_start: 0.7057 (m-10) cc_final: 0.6597 (m-10)
REVERT: B  550 GLU cc_start: 0.8169 (pm20) cc_final: 0.7837 (pm20)
REVERT: B  565 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7659 (tm-30)
REVERT: B  579 ILE cc_start: 0.8141 (tp) cc_final: 0.7906 (tp)
REVERT: B  609 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6790 (t80)
REVERT: B  615 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7584 (tp30)
  outliers start: 30
  outliers final: 25
  residues processed: 103
  average time/residue: 0.0655
  time to fit residues: 9.5664
Evaluate side-chains
  110 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  609 PHE
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.0470
   chunk 52 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.5078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 441 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.167187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.122824 restraints weight = 6900.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.126968 restraints weight = 4305.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.129688 restraints weight = 3271.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.131328 restraints weight = 2774.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.132514 restraints weight = 2509.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6648  Z= 0.133
  Angle     :  0.564   9.287   9046  Z= 0.286
  Chirality :  0.037   0.141    990
  Planarity :  0.004   0.039   1096
  Dihedral  :  3.858  15.005    848
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 21.93 %
    Favored  : 73.25 %
  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:  0.79 (0.32), residues: 762
  helix:  1.75 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -3.11 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 611 
 TYR   0.010   0.001   TYR B 553 
 PHE   0.017   0.001   PHE B 474 
 TRP   0.009   0.001   TRP B 573 
 HIS   0.025   0.001   HIS A 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 6646)
  covalent geometry    : angle       0.56340 /  0.29 ( 9042)
  SS BOND              : bond        0.00090 /  0.06 (    2)
  SS BOND              : angle       1.14426 /  0.68 (    4)
  hydrogen bonds       : bond        0.04002 /  2.66 (  432)
  hydrogen bonds       : angle       3.77166 /  2.82 ( 1290)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 72
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  550 GLU cc_start: 0.8229 (pm20) cc_final: 0.7855 (pm20)
REVERT: A  565 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7694 (tm-30)
REVERT: A  579 ILE cc_start: 0.8161 (tp) cc_final: 0.7938 (tp)
REVERT: A  609 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6701 (t80)
REVERT: A  615 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7352 (tp30)
REVERT: B  375 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6991 (mm)
REVERT: B  550 GLU cc_start: 0.8214 (pm20) cc_final: 0.7847 (pm20)
REVERT: B  565 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7641 (tm-30)
REVERT: B  579 ILE cc_start: 0.8128 (tp) cc_final: 0.7912 (tp)
REVERT: B  609 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6715 (t80)
REVERT: B  615 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7489 (tp30)
  outliers start: 33
  outliers final: 27
  residues processed: 94
  average time/residue: 0.0567
  time to fit residues: 7.9075
Evaluate side-chains
  99 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 69
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain B residue  440 CYS
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  609 PHE
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 441 HIS
** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.165576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.121166 restraints weight = 6961.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.125247 restraints weight = 4400.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.127769 restraints weight = 3358.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.129623 restraints weight = 2861.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.130573 restraints weight = 2576.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6648  Z= 0.153
  Angle     :  0.579   8.505   9046  Z= 0.296
  Chirality :  0.038   0.176    990
  Planarity :  0.004   0.039   1096
  Dihedral  :  3.872  15.260    848
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 21.93 %
    Favored  : 72.95 %
  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:  0.80 (0.32), residues: 762
  helix:  1.76 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -3.12 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 611 
 TYR   0.012   0.001   TYR A 553 
 PHE   0.016   0.001   PHE A 609 
 TRP   0.010   0.001   TRP B 573 
 HIS   0.030   0.002   HIS A 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 ( 6646)
  covalent geometry    : angle       0.57784 /  0.30 ( 9042)
  SS BOND              : bond        0.00077 /  0.05 (    2)
  SS BOND              : angle       1.52594 /  0.87 (    4)
  hydrogen bonds       : bond        0.04223 /  2.81 (  432)
  hydrogen bonds       : angle       3.79640 /  2.85 ( 1290)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 74
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  550 GLU cc_start: 0.8227 (pm20) cc_final: 0.7791 (pm20)
REVERT: A  579 ILE cc_start: 0.8130 (tp) cc_final: 0.7920 (tp)
REVERT: A  609 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6802 (t80)
REVERT: A  615 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7375 (tp30)
REVERT: B  375 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6964 (mm)
REVERT: B  550 GLU cc_start: 0.8202 (pm20) cc_final: 0.7803 (pm20)
REVERT: B  609 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6843 (t80)
REVERT: B  615 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7523 (tp30)
  outliers start: 35
  outliers final: 28
  residues processed: 99
  average time/residue: 0.0555
  time to fit residues: 8.2444
Evaluate side-chains
  105 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain B residue  440 CYS
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  527 ILE
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  609 PHE
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 14 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.7984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS
** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.164429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.119721 restraints weight = 6971.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.123810 restraints weight = 4359.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.126470 restraints weight = 3319.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.128243 restraints weight = 2813.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.129011 restraints weight = 2551.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6648  Z= 0.165
  Angle     :  0.598   8.230   9046  Z= 0.306
  Chirality :  0.039   0.161    990
  Planarity :  0.004   0.039   1096
  Dihedral  :  3.904  15.195    848
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 22.22 %
    Favored  : 72.37 %
  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:  0.77 (0.32), residues: 762
  helix:  1.73 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -3.11 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 611 
 TYR   0.013   0.001   TYR B 553 
 PHE   0.017   0.001   PHE B 609 
 TRP   0.013   0.001   TRP B 573 
 HIS   0.003   0.001   HIS B 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.16 ( 6646)
  covalent geometry    : angle       0.59698 /  0.31 ( 9042)
  SS BOND              : bond        0.00070 /  0.05 (    2)
  SS BOND              : angle       1.39679 /  0.79 (    4)
  hydrogen bonds       : bond        0.04309 /  2.86 (  432)
  hydrogen bonds       : angle       3.81776 /  2.86 ( 1290)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 79
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  550 GLU cc_start: 0.8247 (pm20) cc_final: 0.7822 (pm20)
REVERT: A  609 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6788 (t80)
REVERT: A  615 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7269 (tp30)
REVERT: B  372 PHE cc_start: 0.7778 (m-10) cc_final: 0.7470 (m-80)
REVERT: B  375 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7012 (mm)
REVERT: B  550 GLU cc_start: 0.8218 (pm20) cc_final: 0.7826 (pm20)
REVERT: B  609 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6796 (t80)
REVERT: B  615 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7474 (tp30)
  outliers start: 37
  outliers final: 31
  residues processed: 104
  average time/residue: 0.0603
  time to fit residues: 9.3607
Evaluate side-chains
  113 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 79
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain B residue  440 CYS
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  527 ILE
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  609 PHE
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0370
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.166284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.121742 restraints weight = 7041.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.125929 restraints weight = 4353.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.128510 restraints weight = 3283.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.130449 restraints weight = 2775.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.130835 restraints weight = 2502.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6648  Z= 0.141
  Angle     :  0.578   8.147   9046  Z= 0.294
  Chirality :  0.037   0.144    990
  Planarity :  0.004   0.039   1096
  Dihedral  :  3.835  14.672    848
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 22.81 %
    Favored  : 72.37 %
  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:  0.88 (0.32), residues: 762
  helix:  1.81 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -3.07 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 604 
 TYR   0.011   0.001   TYR B 553 
 PHE   0.014   0.001   PHE B 609 
 TRP   0.012   0.001   TRP A 573 
 HIS   0.003   0.001   HIS B 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 6646)
  covalent geometry    : angle       0.57802 /  0.29 ( 9042)
  SS BOND              : bond        0.00048 /  0.03 (    2)
  SS BOND              : angle       1.09955 /  0.61 (    4)
  hydrogen bonds       : bond        0.04096 /  2.72 (  432)
  hydrogen bonds       : angle       3.75556 /  2.81 ( 1290)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 76
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  550 GLU cc_start: 0.8251 (pm20) cc_final: 0.7816 (pm20)
REVERT: A  609 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6763 (t80)
REVERT: A  615 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7094 (tp30)
REVERT: B  375 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6928 (mm)
REVERT: B  550 GLU cc_start: 0.8229 (pm20) cc_final: 0.7824 (pm20)
REVERT: B  609 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6732 (t80)
REVERT: B  615 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7270 (tp30)
  outliers start: 33
  outliers final: 29
  residues processed: 98
  average time/residue: 0.0622
  time to fit residues: 8.9469
Evaluate side-chains
  107 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 75
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  569 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain B residue  440 CYS
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  609 PHE
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 57 optimal weight:    0.0970
   chunk 15 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 19 optimal weight:   30.0000
   chunk 31 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.168008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.123241 restraints weight = 6855.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.127447 restraints weight = 4247.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.130225 restraints weight = 3216.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.131891 restraints weight = 2726.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.133138 restraints weight = 2466.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6648  Z= 0.133
  Angle     :  0.567   8.109   9046  Z= 0.287
  Chirality :  0.037   0.138    990
  Planarity :  0.004   0.039   1096
  Dihedral  :  3.749  14.441    848
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 22.37 %
    Favored  : 72.51 %
  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:  0.98 (0.32), residues: 762
  helix:  1.89 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -3.04 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 604 
 TYR   0.010   0.001   TYR B 553 
 PHE   0.013   0.001   PHE A 474 
 TRP   0.013   0.001   TRP A 573 
 HIS   0.003   0.001   HIS B 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.13 ( 6646)
  covalent geometry    : angle       0.56678 /  0.29 ( 9042)
  SS BOND              : bond        0.00066 /  0.05 (    2)
  SS BOND              : angle       0.96983 /  0.53 (    4)
  hydrogen bonds       : bond        0.03917 /  2.60 (  432)
  hydrogen bonds       : angle       3.69145 /  2.76 ( 1290)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 72
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  550 GLU cc_start: 0.8271 (pm20) cc_final: 0.7821 (pm20)
REVERT: A  609 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6641 (t80)
REVERT: A  615 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7306 (tp30)
REVERT: B  375 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6965 (mm)
REVERT: B  550 GLU cc_start: 0.8245 (pm20) cc_final: 0.7805 (pm20)
REVERT: B  609 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6681 (t80)
REVERT: B  615 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7223 (tp30)
  outliers start: 35
  outliers final: 29
  residues processed: 98
  average time/residue: 0.0501
  time to fit residues: 7.3893
Evaluate side-chains
  103 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 71
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  409 ASP
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  595 VAL
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  409 ASP
Chi-restraints excluded: chain B residue  440 CYS
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  609 PHE
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0770
   chunk 46 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    0.6738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.165963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.121053 restraints weight = 6913.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.125203 restraints weight = 4312.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.127825 restraints weight = 3275.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.129551 restraints weight = 2780.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.130341 restraints weight = 2515.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6648  Z= 0.151
  Angle     :  0.584   7.932   9046  Z= 0.297
  Chirality :  0.038   0.135    990
  Planarity :  0.004   0.039   1096
  Dihedral  :  3.782  14.442    848
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 22.51 %
    Favored  : 72.51 %
  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:  0.93 (0.32), residues: 762
  helix:  1.84 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -3.03 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 611 
 TYR   0.012   0.001   TYR B 553 
 PHE   0.016   0.001   PHE A 609 
 TRP   0.012   0.001   TRP A 573 
 HIS   0.004   0.001   HIS A 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.15 ( 6646)
  covalent geometry    : angle       0.58409 /  0.30 ( 9042)
  SS BOND              : bond        0.00090 /  0.06 (    2)
  SS BOND              : angle       1.08658 /  0.60 (    4)
  hydrogen bonds       : bond        0.04159 /  2.76 (  432)
  hydrogen bonds       : angle       3.74444 /  2.80 ( 1290)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1063.41 seconds
wall clock time: 19 minutes 4.34 seconds (1144.34 seconds total)