Starting phenix.real_space_refine
on Tue Feb  3 19:31:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jxr_61877/02_2026/9jxr_61877.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jxr_61877/02_2026/9jxr_61877.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jxr_61877/02_2026/9jxr_61877.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jxr_61877/02_2026/9jxr_61877.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jxr_61877/02_2026/9jxr_61877.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jxr_61877/02_2026/9jxr_61877.map"
  }
  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=  -0.000 sd=   0.071
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      46      5.16       5
     C    4244      2.51       5
     N    1016      2.21       5
     O    1044      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6350
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3175
          Classifications: {'peptide': 384}
          Link IDs: {'PTRANS': 16, 'TRANS': 367}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.59, per 1000 atoms: 0.25
  Number of scatterers: 6350
  At special positions: 0
  Unit cell: (96.005, 104.445, 83.345, 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      46     16.00
     O    1044      8.00
     N    1016      7.00
     C    4244      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 406 " - pdb=" SG  CYS A 424 " distance=2.08
    Simple disulfide: pdb=" SG  CYS B 406 " - pdb=" SG  CYS B 424 " distance=2.08

  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: 0.35
  Conformation dependent library (CDL) restraints added in 240.6 milliseconds
  

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      79.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 223 through 250
    Processing helix  chain 'A' and resid 255 through 286
      removed outlier: 4.577A  pdb=" N   ALA A 265 " --> pdb=" O   ARG A 261 " (cutoff:3.500A)
      Proline residue:  A 266  - end of helix
    Processing helix  chain 'A' and resid 289 through 295
      removed outlier: 3.605A  pdb=" N   ILE A 293 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 294 " --> pdb=" O   HIS A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 327
    Processing helix  chain 'A' and resid 327 through 332
    Processing helix  chain 'A' and resid 336 through 351
      removed outlier: 3.656A  pdb=" N   LEU A 340 " --> pdb=" O   TYR A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 374
    Processing helix  chain 'A' and resid 381 through 394
    Processing helix  chain 'A' and resid 395 through 411
      removed outlier: 3.713A  pdb=" N   LEU A 399 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      Proline residue:  A 402  - end of helix
    Processing helix  chain 'A' and resid 420 through 424
      removed outlier: 3.804A  pdb=" N   CYS A 424 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 454
      removed outlier: 3.707A  pdb=" N   VAL A 435 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
      Proline residue:  A 439  - end of helix
      removed outlier: 3.625A  pdb=" N   ARG A 443 " --> pdb=" O   PRO A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 483
      removed outlier: 3.610A  pdb=" N   HIS A 478 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LYS A 479 " --> pdb=" O   ILE A 475 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   TYR A 480 " --> pdb=" O   PHE A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 517
    Processing helix  chain 'A' and resid 540 through 556
      removed outlier: 4.292A  pdb=" N   TYR A 544 " --> pdb=" O   SER A 540 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE A 549 " --> pdb=" O   TYR A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 567
      removed outlier: 4.741A  pdb=" N   SER A 563 " --> pdb=" O   THR A 559 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   LEU A 564 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ILE A 565 " --> pdb=" O   SER A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 606
      removed outlier: 4.310A  pdb=" N   MET A 576 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
      Proline residue:  A 581  - end of helix
    Processing helix  chain 'B' and resid 224 through 250
    Processing helix  chain 'B' and resid 255 through 286
      removed outlier: 4.578A  pdb=" N   ALA B 265 " --> pdb=" O   ARG B 261 " (cutoff:3.500A)
      Proline residue:  B 266  - end of helix
    Processing helix  chain 'B' and resid 289 through 295
      removed outlier: 3.605A  pdb=" N   ILE B 293 " --> pdb=" O   ASN B 289 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   PHE B 294 " --> pdb=" O   HIS B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 327
    Processing helix  chain 'B' and resid 327 through 332
    Processing helix  chain 'B' and resid 336 through 351
      removed outlier: 3.656A  pdb=" N   LEU B 340 " --> pdb=" O   TYR B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 374
    Processing helix  chain 'B' and resid 381 through 394
    Processing helix  chain 'B' and resid 395 through 411
      removed outlier: 3.713A  pdb=" N   LEU B 399 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
      Proline residue:  B 402  - end of helix
    Processing helix  chain 'B' and resid 420 through 424
      removed outlier: 3.804A  pdb=" N   CYS B 424 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 454
      removed outlier: 3.707A  pdb=" N   VAL B 435 " --> pdb=" O   LEU B 431 " (cutoff:3.500A)
      Proline residue:  B 439  - end of helix
      removed outlier: 3.625A  pdb=" N   ARG B 443 " --> pdb=" O   PRO B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 483
      removed outlier: 3.609A  pdb=" N   HIS B 478 " --> pdb=" O   VAL B 474 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LYS B 479 " --> pdb=" O   ILE B 475 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   TYR B 480 " --> pdb=" O   PHE B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 517
    Processing helix  chain 'B' and resid 540 through 556
      removed outlier: 4.293A  pdb=" N   TYR B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE B 549 " --> pdb=" O   TYR B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 567
      removed outlier: 4.741A  pdb=" N   SER B 563 " --> pdb=" O   THR B 559 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   LEU B 564 " --> pdb=" O   LEU B 560 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ILE B 565 " --> pdb=" O   SER B 561 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 606
      removed outlier: 4.310A  pdb=" N   MET B 576 " --> pdb=" O   GLY B 572 " (cutoff:3.500A)
      Proline residue:  B 581  - end of helix

    423 hydrogen bonds defined for protein.
    1263 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: 0.93

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.15 -     1.31: 1216
        1.31 -     1.47: 2814
        1.47 -     1.64: 2470
        1.64 -     1.80: 42
        1.80 -     1.97: 40
  Bond restraints: 6582
  Sorted by residual:
  bond pdb=" CA  TYR B 511 "
       pdb=" C   TYR B 511 "
    ideal  model  delta    sigma   weight residual
    1.524  1.410  0.115 1.28e-02 6.10e+03 8.01e+01
  bond pdb=" CA  TYR A 511 "
       pdb=" C   TYR A 511 "
    ideal  model  delta    sigma   weight residual
    1.524  1.410  0.114 1.28e-02 6.10e+03 7.94e+01
  bond pdb=" CA  SER B 393 "
       pdb=" C   SER B 393 "
    ideal  model  delta    sigma   weight residual
    1.524  1.411  0.112 1.27e-02 6.20e+03 7.83e+01
  bond pdb=" CA  SER A 393 "
       pdb=" C   SER A 393 "
    ideal  model  delta    sigma   weight residual
    1.524  1.411  0.112 1.27e-02 6.20e+03 7.81e+01
  bond pdb=" CA  VAL B 574 "
       pdb=" C   VAL B 574 "
    ideal  model  delta    sigma   weight residual
    1.523  1.633 -0.111 1.28e-02 6.10e+03 7.46e+01
  ... (remaining 6577 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 5972
        2.68 -     5.36: 1847
        5.36 -     8.04: 849
        8.04 -    10.73: 243
       10.73 -    13.41: 55
  Bond angle restraints: 8966
  Sorted by residual:
  angle pdb=" N   VAL B 229 "
        pdb=" CA  VAL B 229 "
        pdb=" C   VAL B 229 "
      ideal   model   delta    sigma   weight residual
     110.72   99.18   11.54 1.01e+00 9.80e-01 1.30e+02
  angle pdb=" N   VAL A 229 "
        pdb=" CA  VAL A 229 "
        pdb=" C   VAL A 229 "
      ideal   model   delta    sigma   weight residual
     110.72   99.21   11.51 1.01e+00 9.80e-01 1.30e+02
  angle pdb=" N   TYR B 544 "
        pdb=" CA  TYR B 544 "
        pdb=" C   TYR B 544 "
      ideal   model   delta    sigma   weight residual
     111.36  100.30   11.06 1.09e+00 8.42e-01 1.03e+02
  angle pdb=" N   TYR A 544 "
        pdb=" CA  TYR A 544 "
        pdb=" C   TYR A 544 "
      ideal   model   delta    sigma   weight residual
     111.36  100.31   11.05 1.09e+00 8.42e-01 1.03e+02
  angle pdb=" N   TRP B 542 "
        pdb=" CA  TRP B 542 "
        pdb=" C   TRP B 542 "
      ideal   model   delta    sigma   weight residual
     111.82  100.09   11.73 1.16e+00 7.43e-01 1.02e+02
  ... (remaining 8961 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.52: 3209
       14.52 -    29.03: 451
       29.03 -    43.55: 50
       43.55 -    58.06: 6
       58.06 -    72.58: 2
  Dihedral angle restraints: 3718
    sinusoidal: 1446
      harmonic: 2272
  Sorted by residual:
  dihedral pdb=" C   SER A 490 "
           pdb=" N   SER A 490 "
           pdb=" CA  SER A 490 "
           pdb=" CB  SER A 490 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -158.29   35.69     0      2.50e+00 1.60e-01 2.04e+02
  dihedral pdb=" C   SER B 490 "
           pdb=" N   SER B 490 "
           pdb=" CA  SER B 490 "
           pdb=" CB  SER B 490 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -158.26   35.66     0      2.50e+00 1.60e-01 2.03e+02
  dihedral pdb=" N   SER A 490 "
           pdb=" C   SER A 490 "
           pdb=" CA  SER A 490 "
           pdb=" CB  SER A 490 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  158.19  -35.39     0      2.50e+00 1.60e-01 2.00e+02
  ... (remaining 3715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.332: 664
       0.332 -    0.663: 210
       0.663 -    0.994: 59
       0.994 -    1.326: 13
       1.326 -    1.657: 4
  Chirality restraints: 950
  Sorted by residual:
  chirality pdb=" CA  SER A 490 "
            pdb=" N   SER A 490 "
            pdb=" C   SER A 490 "
            pdb=" CB  SER A 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.85    1.66 2.00e-01 2.50e+01 6.86e+01
  chirality pdb=" CA  SER B 490 "
            pdb=" N   SER B 490 "
            pdb=" C   SER B 490 "
            pdb=" CB  SER B 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.85    1.66 2.00e-01 2.50e+01 6.86e+01
  chirality pdb=" CA  TYR B 511 "
            pdb=" N   TYR B 511 "
            pdb=" C   TYR B 511 "
            pdb=" CB  TYR B 511 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.12    1.39 2.00e-01 2.50e+01 4.84e+01
  ... (remaining 947 not shown)

  Planarity restraints: 1104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 558 "    0.346 2.00e-02 2.50e+03   2.33e-01 1.36e+03
        pdb=" CG  TRP B 558 "    0.107 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 558 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 558 "   -0.272 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 558 "   -0.154 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 558 "   -0.153 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 558 "   -0.325 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 558 "    0.293 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 558 "   -0.085 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 558 "    0.300 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 558 "    0.346 2.00e-02 2.50e+03   2.33e-01 1.36e+03
        pdb=" CG  TRP A 558 "    0.107 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 558 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 558 "   -0.272 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 558 "   -0.154 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 558 "   -0.153 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 558 "   -0.325 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 558 "    0.293 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 558 "   -0.085 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 558 "    0.300 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 499 "    0.124 2.00e-02 2.50e+03   1.26e-01 3.96e+02
        pdb=" CG  TRP A 499 "    0.129 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 499 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 499 "   -0.064 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 499 "   -0.165 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 499 "   -0.069 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 499 "   -0.168 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 499 "    0.158 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 499 "   -0.097 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 499 "    0.165 2.00e-02 2.50e+03
  ... (remaining 1101 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 2440
        2.88 -     3.39: 7136
        3.39 -     3.89: 10449
        3.89 -     4.40: 12286
        4.40 -     4.90: 19120
  Nonbonded interactions: 51431
  Sorted by model distance:
  nonbonded pdb=" N   LEU B 302 "
            pdb=" O   LEU B 302 "
     model   vdw
     2.381 2.496
  nonbonded pdb=" N   LEU A 302 "
            pdb=" O   LEU A 302 "
     model   vdw
     2.381 2.496
  nonbonded pdb=" N   HIS B 415 "
            pdb=" O   HIS B 415 "
     model   vdw
     2.416 2.496
  nonbonded pdb=" N   HIS A 415 "
            pdb=" O   HIS A 415 "
     model   vdw
     2.417 2.496
  nonbonded pdb=" CD  GLU A 571 "
            pdb=" N   GLY A 572 "
     model   vdw
     2.417 3.350
  ... (remaining 51426 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:             2.280
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.160
  Find NCS groups from input model:        0.050
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
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      :  0.041   0.175   6584  Z= 2.610
  Angle     :  3.343  13.407   8970  Z= 2.311
  Chirality :  0.361   1.657    950
  Planarity :  0.029   0.233   1104
  Dihedral  : 11.655  72.581   2244
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  1.20 %
    Favored  : 98.20 %
  Cbeta Deviations : 21.53 %
  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: -2.49 (0.28), residues: 764
  helix: -1.21 (0.20), residues: 564
  sheet:  None (None), residues: 0
  loop : -2.53 (0.40), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.062   0.011   ARG B 371 
 TYR   0.149   0.039   TYR B 487 
 PHE   0.133   0.034   PHE B 496 
 TRP   0.346   0.058   TRP B 558 
 HIS   0.079   0.027   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.04108 ( 6582)
  covalent geometry    : angle       3.34368 ( 8966)
  SS BOND              : bond        0.05085 (    2)
  SS BOND              : angle       2.35162 (    4)
  hydrogen bonds       : bond        0.13322 (  423)
  hydrogen bonds       : angle       6.26996 ( 1263)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 262
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  261 ARG cc_start: 0.8467 (mmt90) cc_final: 0.8143 (mtp85)
REVERT: A  301 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7278 (p-80)
REVERT: A  306 ASN cc_start: 0.8155 (m-40) cc_final: 0.7949 (m-40)
REVERT: A  355 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7813 (ttmm)
REVERT: A  480 TYR cc_start: 0.7082 (t80) cc_final: 0.5825 (t80)
REVERT: A  492 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8317 (mt-10)
REVERT: A  523 ASP cc_start: 0.7575 (t0) cc_final: 0.7338 (t0)
REVERT: A  530 ARG cc_start: 0.7741 (ttm170) cc_final: 0.6775 (mtm180)
REVERT: A  534 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8178 (mp0)
REVERT: A  542 TRP cc_start: 0.6863 (p-90) cc_final: 0.6461 (p-90)
REVERT: A  583 GLU cc_start: 0.8268 (tp30) cc_final: 0.7884 (tp30)
REVERT: B  261 ARG cc_start: 0.8466 (mmt90) cc_final: 0.8239 (mtp85)
REVERT: B  279 ASN cc_start: 0.8499 (t0) cc_final: 0.8285 (t0)
REVERT: B  355 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8043 (ttmm)
REVERT: B  480 TYR cc_start: 0.7150 (t80) cc_final: 0.5978 (t80)
REVERT: B  492 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8212 (mt-10)
REVERT: B  530 ARG cc_start: 0.7686 (ttm170) cc_final: 0.6763 (mtm180)
REVERT: B  534 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7972 (mm-30)
REVERT: B  535 GLU cc_start: 0.8672 (mp0) cc_final: 0.8466 (pm20)
REVERT: B  583 GLU cc_start: 0.8339 (tp30) cc_final: 0.7968 (tp30)
  outliers start: 4
  outliers final: 3
  residues processed: 262
  average time/residue: 0.0790
  time to fit residues: 26.8187
Evaluate side-chains
  163 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 159
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 HIS
Chi-restraints excluded: chain A residue  476 PHE
Chi-restraints excluded: chain B residue  301 HIS
Chi-restraints excluded: chain B residue  476 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 300 ASN
A 301 HIS
A 446 GLN
A 601 ASN
B 279 ASN
B 300 ASN
B 301 HIS
B 306 ASN
B 601 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.167208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.138268 restraints weight = 9802.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142651 restraints weight = 4816.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.145455 restraints weight = 3165.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.147234 restraints weight = 2470.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.148158 restraints weight = 2114.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6584  Z= 0.194
  Angle     :  0.774  10.050   8970  Z= 0.407
  Chirality :  0.045   0.213    950
  Planarity :  0.006   0.048   1104
  Dihedral  :  6.031  37.114    850
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 10.78 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  1.18 (0.31), residues: 764
  helix:  1.43 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -1.40 (0.53), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 533 
 TYR   0.040   0.003   TYR A 487 
 PHE   0.027   0.002   PHE B 458 
 TRP   0.015   0.002   TRP B 414 
 HIS   0.007   0.002   HIS A 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 6582)
  covalent geometry    : angle       0.77442 ( 8966)
  SS BOND              : bond        0.00114 (    2)
  SS BOND              : angle       0.29583 (    4)
  hydrogen bonds       : bond        0.05444 (  423)
  hydrogen bonds       : angle       4.26362 ( 1263)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 167
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  474 VAL cc_start: 0.8622 (t) cc_final: 0.8347 (p)
REVERT: A  530 ARG cc_start: 0.7648 (ttm170) cc_final: 0.6736 (mtm180)
REVERT: A  534 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8123 (mp0)
REVERT: A  583 GLU cc_start: 0.8425 (tp30) cc_final: 0.7892 (tp30)
REVERT: A  605 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7980 (tptt)
REVERT: B  362 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7129 (mmp-170)
REVERT: B  523 ASP cc_start: 0.7334 (t0) cc_final: 0.6649 (t70)
REVERT: B  530 ARG cc_start: 0.7620 (ttm170) cc_final: 0.6750 (mtm180)
REVERT: B  535 GLU cc_start: 0.8632 (mp0) cc_final: 0.8412 (pm20)
REVERT: B  551 ASP cc_start: 0.8614 (t0) cc_final: 0.8396 (t0)
REVERT: B  583 GLU cc_start: 0.8436 (tp30) cc_final: 0.7909 (tp30)
  outliers start: 29
  outliers final: 16
  residues processed: 182
  average time/residue: 0.0604
  time to fit residues: 15.1473
Evaluate side-chains
  158 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  529 ASN
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  458 PHE
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 446 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.167636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.138798 restraints weight = 9854.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.143103 restraints weight = 4777.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.145903 restraints weight = 3143.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.147588 restraints weight = 2450.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.148386 restraints weight = 2112.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6584  Z= 0.151
  Angle     :  0.646   7.346   8970  Z= 0.341
  Chirality :  0.042   0.155    950
  Planarity :  0.005   0.042   1104
  Dihedral  :  5.196  30.181    842
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 12.57 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  2.13 (0.31), residues: 764
  helix:  2.36 (0.21), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.62 (0.47), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 261 
 TYR   0.025   0.002   TYR B 592 
 PHE   0.026   0.002   PHE A 458 
 TRP   0.024   0.002   TRP A 495 
 HIS   0.005   0.001   HIS A 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6582)
  covalent geometry    : angle       0.64613 ( 8966)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       0.25309 (    4)
  hydrogen bonds       : bond        0.04676 (  423)
  hydrogen bonds       : angle       4.03214 ( 1263)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  295 GLU cc_start: 0.7411 (tt0) cc_final: 0.7202 (tm-30)
REVERT: A  474 VAL cc_start: 0.8641 (t) cc_final: 0.8404 (p)
REVERT: A  495 TRP cc_start: 0.6638 (t60) cc_final: 0.6431 (t60)
REVERT: A  528 ASP cc_start: 0.8294 (t0) cc_final: 0.8022 (t0)
REVERT: A  530 ARG cc_start: 0.7633 (ttm170) cc_final: 0.6681 (mtm180)
REVERT: A  566 GLU cc_start: 0.7681 (tp30) cc_final: 0.6512 (pt0)
REVERT: A  583 GLU cc_start: 0.8359 (tp30) cc_final: 0.8012 (tp30)
REVERT: B  295 GLU cc_start: 0.7453 (tt0) cc_final: 0.7215 (tm-30)
REVERT: B  474 VAL cc_start: 0.8562 (t) cc_final: 0.8304 (p)
REVERT: B  530 ARG cc_start: 0.7668 (ttm170) cc_final: 0.6718 (mtm180)
REVERT: B  535 GLU cc_start: 0.8789 (mp0) cc_final: 0.8484 (pm20)
REVERT: B  551 ASP cc_start: 0.8668 (t0) cc_final: 0.8386 (t0)
REVERT: B  566 GLU cc_start: 0.7846 (tp30) cc_final: 0.6334 (pt0)
REVERT: B  583 GLU cc_start: 0.8361 (tp30) cc_final: 0.7959 (tp30)
  outliers start: 31
  outliers final: 24
  residues processed: 175
  average time/residue: 0.0658
  time to fit residues: 15.9224
Evaluate side-chains
  160 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  458 PHE
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  438 MET
Chi-restraints excluded: chain B residue  458 PHE
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 ILE
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 61 optimal weight:    0.1980
   chunk 10 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 70 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 415 HIS
A 432 HIS
B 446 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.166495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.138158 restraints weight = 9989.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.142254 restraints weight = 5073.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.144978 restraints weight = 3424.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.146339 restraints weight = 2703.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.147539 restraints weight = 2367.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6584  Z= 0.150
  Angle     :  0.662  15.017   8970  Z= 0.337
  Chirality :  0.041   0.137    950
  Planarity :  0.005   0.038   1104
  Dihedral  :  4.956  27.636    842
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 15.57 %
    Favored  : 80.84 %
  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:  2.22 (0.31), residues: 764
  helix:  2.33 (0.21), residues: 584
  sheet:  None (None), residues: 0
  loop : -1.55 (0.50), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 533 
 TYR   0.022   0.002   TYR B 592 
 PHE   0.022   0.001   PHE B 458 
 TRP   0.017   0.001   TRP B 495 
 HIS   0.008   0.001   HIS A 432 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6582)
  covalent geometry    : angle       0.66226 ( 8966)
  SS BOND              : bond        0.00139 (    2)
  SS BOND              : angle       0.42132 (    4)
  hydrogen bonds       : bond        0.04393 (  423)
  hydrogen bonds       : angle       4.00563 ( 1263)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  438 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7946 (ttm)
REVERT: A  474 VAL cc_start: 0.8651 (t) cc_final: 0.8445 (p)
REVERT: A  528 ASP cc_start: 0.8216 (t0) cc_final: 0.7847 (t0)
REVERT: A  530 ARG cc_start: 0.7768 (ttm170) cc_final: 0.6786 (mtm180)
REVERT: A  566 GLU cc_start: 0.7550 (tp30) cc_final: 0.6541 (pt0)
REVERT: A  573 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6734 (m-30)
REVERT: A  583 GLU cc_start: 0.8332 (tp30) cc_final: 0.8061 (tp30)
REVERT: B  438 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7846 (ttm)
REVERT: B  530 ARG cc_start: 0.7769 (ttm170) cc_final: 0.6839 (mtm180)
REVERT: B  551 ASP cc_start: 0.8587 (t0) cc_final: 0.8296 (t0)
REVERT: B  566 GLU cc_start: 0.7690 (tp30) cc_final: 0.6416 (pt0)
REVERT: B  583 GLU cc_start: 0.8336 (tp30) cc_final: 0.8047 (tp30)
  outliers start: 24
  outliers final: 17
  residues processed: 161
  average time/residue: 0.0628
  time to fit residues: 14.2271
Evaluate side-chains
  151 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  573 ASP
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  438 MET
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0000
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 446 GLN
B 460 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.166622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.137432 restraints weight = 10053.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.141800 restraints weight = 4855.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.144721 restraints weight = 3191.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.146399 restraints weight = 2483.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.147467 restraints weight = 2149.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6584  Z= 0.152
  Angle     :  0.632  10.954   8970  Z= 0.326
  Chirality :  0.041   0.139    950
  Planarity :  0.005   0.039   1104
  Dihedral  :  4.846  25.883    842
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 15.87 %
    Favored  : 79.79 %
  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:  2.25 (0.31), residues: 764
  helix:  2.50 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.62 (0.48), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 450 
 TYR   0.024   0.002   TYR B 511 
 PHE   0.017   0.001   PHE B 458 
 TRP   0.009   0.001   TRP B 495 
 HIS   0.004   0.001   HIS B 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 6582)
  covalent geometry    : angle       0.63219 ( 8966)
  SS BOND              : bond        0.00085 (    2)
  SS BOND              : angle       0.37178 (    4)
  hydrogen bonds       : bond        0.04330 (  423)
  hydrogen bonds       : angle       3.97456 ( 1263)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  446 GLN cc_start: 0.9157 (mt0) cc_final: 0.8907 (mt0)
REVERT: A  474 VAL cc_start: 0.8578 (t) cc_final: 0.8357 (p)
REVERT: A  495 TRP cc_start: 0.6772 (t60) cc_final: 0.6518 (t60)
REVERT: A  517 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8093 (mtp)
REVERT: A  528 ASP cc_start: 0.8226 (t0) cc_final: 0.7850 (t0)
REVERT: A  530 ARG cc_start: 0.7779 (ttm170) cc_final: 0.6790 (mtm180)
REVERT: A  566 GLU cc_start: 0.7590 (tp30) cc_final: 0.6452 (pt0)
REVERT: A  583 GLU cc_start: 0.8354 (tp30) cc_final: 0.8043 (tp30)
REVERT: B  281 TYR cc_start: 0.7559 (t80) cc_final: 0.7315 (t80)
REVERT: B  438 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8000 (ttm)
REVERT: B  517 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8127 (mtp)
REVERT: B  530 ARG cc_start: 0.7701 (ttm170) cc_final: 0.6748 (mtm180)
REVERT: B  551 ASP cc_start: 0.8683 (t0) cc_final: 0.8431 (t0)
REVERT: B  566 GLU cc_start: 0.7611 (tp30) cc_final: 0.6441 (pt0)
REVERT: B  583 GLU cc_start: 0.8324 (tp30) cc_final: 0.7968 (tp30)
  outliers start: 29
  outliers final: 20
  residues processed: 161
  average time/residue: 0.0607
  time to fit residues: 13.6708
Evaluate side-chains
  159 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  438 MET
Chi-restraints excluded: chain B residue  517 MET
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 460 HIS
B 279 ASN
B 446 GLN
B 460 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.164876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.136147 restraints weight = 10069.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.140254 restraints weight = 5143.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.142871 restraints weight = 3480.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.144584 restraints weight = 2768.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.144940 restraints weight = 2400.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.4263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6584  Z= 0.146
  Angle     :  0.610   9.620   8970  Z= 0.314
  Chirality :  0.041   0.137    950
  Planarity :  0.004   0.040   1104
  Dihedral  :  4.757  26.154    842
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.37 %
    Favored  : 79.34 %
  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:  2.33 (0.32), residues: 764
  helix:  2.57 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.67 (0.48), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 450 
 TYR   0.016   0.002   TYR B 487 
 PHE   0.016   0.001   PHE B 385 
 TRP   0.010   0.001   TRP B 495 
 HIS   0.004   0.001   HIS A 432 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6582)
  covalent geometry    : angle       0.61023 ( 8966)
  SS BOND              : bond        0.00117 (    2)
  SS BOND              : angle       0.43758 (    4)
  hydrogen bonds       : bond        0.04245 (  423)
  hydrogen bonds       : angle       3.90609 ( 1263)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  438 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8050 (ttm)
REVERT: A  446 GLN cc_start: 0.9033 (mt0) cc_final: 0.8830 (mt0)
REVERT: A  495 TRP cc_start: 0.6788 (t60) cc_final: 0.6523 (t60)
REVERT: A  517 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8107 (mtp)
REVERT: A  528 ASP cc_start: 0.8212 (t0) cc_final: 0.7821 (t0)
REVERT: A  530 ARG cc_start: 0.7803 (ttm170) cc_final: 0.6785 (mtm180)
REVERT: A  566 GLU cc_start: 0.7599 (tp30) cc_final: 0.6465 (pt0)
REVERT: A  583 GLU cc_start: 0.8358 (tp30) cc_final: 0.8075 (tp30)
REVERT: B  281 TYR cc_start: 0.7590 (t80) cc_final: 0.7349 (t80)
REVERT: B  438 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7968 (ttm)
REVERT: B  446 GLN cc_start: 0.9189 (mt0) cc_final: 0.8946 (mt0)
REVERT: B  517 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8123 (mtp)
REVERT: B  530 ARG cc_start: 0.7688 (ttm170) cc_final: 0.6711 (mtm180)
REVERT: B  566 GLU cc_start: 0.7589 (tp30) cc_final: 0.6303 (pt0)
REVERT: B  583 GLU cc_start: 0.8317 (tp30) cc_final: 0.8036 (tp30)
  outliers start: 22
  outliers final: 17
  residues processed: 151
  average time/residue: 0.0566
  time to fit residues: 12.1004
Evaluate side-chains
  153 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  279 ASN
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  438 MET
Chi-restraints excluded: chain B residue  517 MET
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   chunk 33 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 39 optimal weight:    0.2980
   chunk 31 optimal weight:    0.0870
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 460 HIS
B 460 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.166159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.137229 restraints weight = 10035.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.141499 restraints weight = 5119.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.144219 restraints weight = 3443.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.145869 restraints weight = 2724.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.146950 restraints weight = 2363.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.4392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6584  Z= 0.140
  Angle     :  0.619   8.662   8970  Z= 0.321
  Chirality :  0.041   0.135    950
  Planarity :  0.004   0.037   1104
  Dihedral  :  4.717  25.221    842
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.11 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.32), residues: 764
  helix:  2.59 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -1.63 (0.48), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 443 
 TYR   0.017   0.002   TYR B 487 
 PHE   0.015   0.001   PHE B 385 
 TRP   0.011   0.001   TRP A 283 
 HIS   0.003   0.001   HIS B 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6582)
  covalent geometry    : angle       0.61909 ( 8966)
  SS BOND              : bond        0.00113 (    2)
  SS BOND              : angle       0.50526 (    4)
  hydrogen bonds       : bond        0.04153 (  423)
  hydrogen bonds       : angle       3.86914 ( 1263)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  438 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8000 (ttm)
REVERT: A  495 TRP cc_start: 0.6745 (t60) cc_final: 0.6518 (t60)
REVERT: A  517 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8122 (mtp)
REVERT: A  528 ASP cc_start: 0.8140 (t0) cc_final: 0.7753 (t0)
REVERT: A  530 ARG cc_start: 0.7873 (ttm170) cc_final: 0.6918 (mtm180)
REVERT: A  566 GLU cc_start: 0.7500 (tp30) cc_final: 0.6488 (pt0)
REVERT: A  583 GLU cc_start: 0.8333 (tp30) cc_final: 0.8092 (tp30)
REVERT: B  426 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7596 (mp0)
REVERT: B  438 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7947 (ttm)
REVERT: B  446 GLN cc_start: 0.9123 (mt0) cc_final: 0.8849 (mt0)
REVERT: B  517 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8127 (mtp)
REVERT: B  530 ARG cc_start: 0.7746 (ttm170) cc_final: 0.6817 (mtm180)
REVERT: B  566 GLU cc_start: 0.7509 (tp30) cc_final: 0.6457 (pt0)
REVERT: B  583 GLU cc_start: 0.8318 (tp30) cc_final: 0.8088 (tp30)
  outliers start: 24
  outliers final: 16
  residues processed: 153
  average time/residue: 0.0544
  time to fit residues: 11.8135
Evaluate side-chains
  156 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  592 TYR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  438 MET
Chi-restraints excluded: chain B residue  517 MET
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 39 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0670
   chunk 52 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
A 460 HIS
B 279 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.165120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.135627 restraints weight = 10069.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.139810 restraints weight = 5162.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.142463 restraints weight = 3506.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.144200 restraints weight = 2792.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.145206 restraints weight = 2428.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.4510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6584  Z= 0.144
  Angle     :  0.608   7.112   8970  Z= 0.317
  Chirality :  0.041   0.138    950
  Planarity :  0.004   0.038   1104
  Dihedral  :  4.662  25.104    842
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 18.26 %
    Favored  : 77.99 %
  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:  2.29 (0.32), residues: 764
  helix:  2.63 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -1.65 (0.45), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 443 
 TYR   0.016   0.002   TYR B 487 
 PHE   0.015   0.001   PHE A 588 
 TRP   0.017   0.001   TRP B 495 
 HIS   0.003   0.001   HIS A 432 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6582)
  covalent geometry    : angle       0.60810 ( 8966)
  SS BOND              : bond        0.00147 (    2)
  SS BOND              : angle       0.59015 (    4)
  hydrogen bonds       : bond        0.04214 (  423)
  hydrogen bonds       : angle       3.92624 ( 1263)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A  438 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8032 (ttm)
REVERT: A  453 ASP cc_start: 0.8670 (t0) cc_final: 0.8376 (t0)
REVERT: A  474 VAL cc_start: 0.8608 (t) cc_final: 0.8334 (p)
REVERT: A  517 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8050 (mtp)
REVERT: A  528 ASP cc_start: 0.8178 (t0) cc_final: 0.7809 (t0)
REVERT: A  530 ARG cc_start: 0.7878 (ttm170) cc_final: 0.6853 (mtm180)
REVERT: A  566 GLU cc_start: 0.7537 (tp30) cc_final: 0.6450 (pt0)
REVERT: A  583 GLU cc_start: 0.8375 (tp30) cc_final: 0.8114 (tp30)
REVERT: B  426 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7652 (mp0)
REVERT: B  438 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8020 (ttm)
REVERT: B  446 GLN cc_start: 0.9123 (mt0) cc_final: 0.8849 (mt0)
REVERT: B  517 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8066 (mtp)
REVERT: B  530 ARG cc_start: 0.7752 (ttm170) cc_final: 0.6824 (mtm180)
REVERT: B  566 GLU cc_start: 0.7551 (tp30) cc_final: 0.6223 (pt0)
REVERT: B  570 ILE cc_start: 0.8414 (tt) cc_final: 0.8020 (mm)
REVERT: B  575 MET cc_start: 0.7797 (tpp) cc_final: 0.7452 (tpp)
REVERT: B  583 GLU cc_start: 0.8311 (tp30) cc_final: 0.8068 (tp30)
  outliers start: 25
  outliers final: 16
  residues processed: 156
  average time/residue: 0.0565
  time to fit residues: 12.5092
Evaluate side-chains
  153 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  592 TYR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  279 ASN
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  438 MET
Chi-restraints excluded: chain B residue  517 MET
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0870
   chunk 31 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0010
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4364

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 460 HIS
A 601 ASN
B 279 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.168976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.139110 restraints weight = 9973.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.143366 restraints weight = 5030.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.146144 restraints weight = 3390.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.147734 restraints weight = 2685.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.148769 restraints weight = 2339.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.4589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6584  Z= 0.138
  Angle     :  0.617   9.672   8970  Z= 0.323
  Chirality :  0.041   0.136    950
  Planarity :  0.004   0.036   1104
  Dihedral  :  4.643  24.203    842
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.01 %
    Favored  : 77.99 %
  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:  2.34 (0.32), residues: 764
  helix:  2.58 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -1.60 (0.48), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 450 
 TYR   0.017   0.002   TYR A 281 
 PHE   0.015   0.001   PHE A 385 
 TRP   0.032   0.001   TRP A 495 
 HIS   0.006   0.001   HIS B 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6582)
  covalent geometry    : angle       0.61736 ( 8966)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       0.60360 (    4)
  hydrogen bonds       : bond        0.04121 (  423)
  hydrogen bonds       : angle       3.88378 ( 1263)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: A  438 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7976 (ttm)
REVERT: A  453 ASP cc_start: 0.8587 (t0) cc_final: 0.8314 (t0)
REVERT: A  517 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8044 (mtp)
REVERT: A  528 ASP cc_start: 0.8102 (t0) cc_final: 0.7727 (t0)
REVERT: A  530 ARG cc_start: 0.7881 (ttm170) cc_final: 0.6896 (mtm180)
REVERT: A  566 GLU cc_start: 0.7520 (tp30) cc_final: 0.6434 (pt0)
REVERT: A  583 GLU cc_start: 0.8334 (tp30) cc_final: 0.8101 (tp30)
REVERT: B  426 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7808 (mp0)
REVERT: B  438 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7963 (ttm)
REVERT: B  446 GLN cc_start: 0.9119 (mt0) cc_final: 0.8844 (mt0)
REVERT: B  517 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8067 (mtp)
REVERT: B  530 ARG cc_start: 0.7751 (ttm170) cc_final: 0.6839 (mtm180)
REVERT: B  566 GLU cc_start: 0.7506 (tp30) cc_final: 0.6189 (pt0)
REVERT: B  570 ILE cc_start: 0.8441 (tt) cc_final: 0.7940 (mm)
REVERT: B  583 GLU cc_start: 0.8303 (tp30) cc_final: 0.8084 (tp30)
  outliers start: 20
  outliers final: 16
  residues processed: 144
  average time/residue: 0.0552
  time to fit residues: 11.2875
Evaluate side-chains
  155 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  592 TYR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  279 ASN
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  438 MET
Chi-restraints excluded: chain B residue  517 MET
Chi-restraints excluded: chain B residue  592 TYR
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 30 optimal weight:    0.0770
   chunk 39 optimal weight:    0.4980
   chunk 73 optimal weight:    0.0980
   chunk 21 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 460 HIS
A 601 ASN
B 279 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.169866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.139672 restraints weight = 9749.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.144051 restraints weight = 4856.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.146839 restraints weight = 3236.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.148570 restraints weight = 2549.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.149396 restraints weight = 2208.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.4670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6584  Z= 0.135
  Angle     :  0.614   7.461   8970  Z= 0.320
  Chirality :  0.040   0.135    950
  Planarity :  0.004   0.036   1104
  Dihedral  :  4.595  24.324    842
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.01 %
    Favored  : 77.84 %
  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:  2.32 (0.31), residues: 764
  helix:  2.65 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -1.64 (0.45), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 443 
 TYR   0.016   0.002   TYR B 487 
 PHE   0.014   0.001   PHE A 385 
 TRP   0.027   0.001   TRP B 495 
 HIS   0.006   0.001   HIS B 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6582)
  covalent geometry    : angle       0.61414 ( 8966)
  SS BOND              : bond        0.00150 (    2)
  SS BOND              : angle       0.67532 (    4)
  hydrogen bonds       : bond        0.04101 (  423)
  hydrogen bonds       : angle       3.88858 ( 1263)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A  438 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7902 (ttm)
REVERT: A  453 ASP cc_start: 0.8510 (t0) cc_final: 0.8249 (t0)
REVERT: A  517 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8033 (mtp)
REVERT: A  528 ASP cc_start: 0.8019 (t0) cc_final: 0.7662 (t0)
REVERT: A  530 ARG cc_start: 0.7885 (ttm170) cc_final: 0.6890 (mtm180)
REVERT: A  566 GLU cc_start: 0.7522 (tp30) cc_final: 0.6449 (pt0)
REVERT: B  426 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7824 (mp0)
REVERT: B  438 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7858 (ttm)
REVERT: B  517 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8046 (mtp)
REVERT: B  530 ARG cc_start: 0.7804 (ttm170) cc_final: 0.6748 (mtm180)
REVERT: B  566 GLU cc_start: 0.7498 (tp30) cc_final: 0.6242 (pt0)
REVERT: B  570 ILE cc_start: 0.8432 (tt) cc_final: 0.7920 (mm)
  outliers start: 21
  outliers final: 15
  residues processed: 146
  average time/residue: 0.0551
  time to fit residues: 11.3277
Evaluate side-chains
  153 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  438 MET
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  592 TYR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  290 HIS
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  438 MET
Chi-restraints excluded: chain B residue  517 MET
Chi-restraints excluded: chain B residue  592 TYR
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 ASN
B 279 ASN
B 446 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.166807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.136380 restraints weight = 9951.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.140600 restraints weight = 5139.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.143149 restraints weight = 3500.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.144974 restraints weight = 2813.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.145828 restraints weight = 2442.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.4696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6584  Z= 0.163
  Angle     :  0.649   9.700   8970  Z= 0.338
  Chirality :  0.042   0.187    950
  Planarity :  0.004   0.040   1104
  Dihedral  :  4.569  23.762    842
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.46 %
    Favored  : 77.54 %
  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:  2.30 (0.31), residues: 764
  helix:  2.65 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -1.68 (0.45), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 450 
 TYR   0.018   0.002   TYR B 281 
 PHE   0.019   0.001   PHE B 531 
 TRP   0.020   0.001   TRP B 495 
 HIS   0.006   0.001   HIS B 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6582)
  covalent geometry    : angle       0.64946 ( 8966)
  SS BOND              : bond        0.00071 (    2)
  SS BOND              : angle       0.56776 (    4)
  hydrogen bonds       : bond        0.04286 (  423)
  hydrogen bonds       : angle       3.99667 ( 1263)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1111.09 seconds
wall clock time: 19 minutes 48.69 seconds (1188.69 seconds total)