Starting phenix.real_space_refine
on Fri Aug 22 23:55:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t57_41044/08_2025/8t57_41044.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t57_41044/08_2025/8t57_41044.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t57_41044/08_2025/8t57_41044.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t57_41044/08_2025/8t57_41044.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t57_41044/08_2025/8t57_41044.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t57_41044/08_2025/8t57_41044.map"
  }
  resolution = 2.7
  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=   0.004
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      26      5.16       5
     C    5752      2.51       5
     N    1270      2.21       5
     O    1418      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8466
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4033
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 4033
          Classifications: {'peptide': 504}
          Link IDs: {'PTRANS': 29, 'TRANS': 474}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 200
          Unusual residues: {'CLR': 2, 'PLM': 8}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.23, per 1000 atoms: 0.38
  Number of scatterers: 8466
  At special positions: 0
  Unit cell: (85.49, 120.51, 85.49, 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      26     16.00
     O    1418      8.00
     N    1270      7.00
     C    5752      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 437.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1936

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 2 sheets defined
      80.9% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 25
    Processing helix  chain 'A' and resid 66 through 71
    Processing helix  chain 'A' and resid 73 through 81
    Processing helix  chain 'A' and resid 82 through 109
    Processing helix  chain 'A' and resid 110 through 115
    Processing helix  chain 'A' and resid 130 through 139
      removed outlier: 6.746A  pdb=" N   ILE A 136 " --> pdb=" O   ASN A 133 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   SER A 137 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 182
      removed outlier: 3.611A  pdb=" N   HIS A 149 " --> pdb=" O   LYS A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 188
    Processing helix  chain 'A' and resid 203 through 216
    Processing helix  chain 'A' and resid 310 through 320
    Processing helix  chain 'A' and resid 336 through 340
      removed outlier: 3.783A  pdb=" N   VAL A 340 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 347
      removed outlier: 3.614A  pdb=" N   ALA A 347 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 368
    Processing helix  chain 'A' and resid 411 through 420
      removed outlier: 3.502A  pdb=" N   PHE A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 431
    Processing helix  chain 'A' and resid 437 through 457
    Processing helix  chain 'A' and resid 457 through 463
    Processing helix  chain 'A' and resid 466 through 474
    Processing helix  chain 'A' and resid 475 through 478
      removed outlier: 6.597A  pdb=" N   LYS A 478 " --> pdb=" O   LEU A 475 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 475 through 478'
    Processing helix  chain 'A' and resid 479 through 486
    Processing helix  chain 'A' and resid 488 through 490
      No H-bonds generated for 'chain 'A' and resid 488 through 490'
    Processing helix  chain 'A' and resid 491 through 512
    Processing helix  chain 'A' and resid 540 through 562
      Proline residue:  A 546  - end of helix
      removed outlier: 3.908A  pdb=" N   PHE A 560 " --> pdb=" O   ILE A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 587
    Processing helix  chain 'A' and resid 598 through 624
    Processing helix  chain 'A' and resid 626 through 633
    Processing helix  chain 'A' and resid 634 through 651
      removed outlier: 3.565A  pdb=" N   VAL A 638 " --> pdb=" O   ILE A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 656
    Processing helix  chain 'A' and resid 659 through 674
      removed outlier: 3.671A  pdb=" N   ARG A 672 " --> pdb=" O   LYS A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 684
      removed outlier: 4.083A  pdb=" N   SER A 681 " --> pdb=" O   SER A 677 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 73 through 81
    Processing helix  chain 'B' and resid 82 through 109
    Processing helix  chain 'B' and resid 110 through 115
    Processing helix  chain 'B' and resid 130 through 139
      removed outlier: 6.746A  pdb=" N   ILE B 136 " --> pdb=" O   ASN B 133 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   SER B 137 " --> pdb=" O   PHE B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 182
      removed outlier: 3.611A  pdb=" N   HIS B 149 " --> pdb=" O   LYS B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 188
    Processing helix  chain 'B' and resid 203 through 216
    Processing helix  chain 'B' and resid 310 through 320
    Processing helix  chain 'B' and resid 336 through 340
      removed outlier: 3.782A  pdb=" N   VAL B 340 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 347
      removed outlier: 3.614A  pdb=" N   ALA B 347 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 368
    Processing helix  chain 'B' and resid 411 through 420
      removed outlier: 3.502A  pdb=" N   PHE B 415 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 431
    Processing helix  chain 'B' and resid 437 through 457
    Processing helix  chain 'B' and resid 457 through 463
    Processing helix  chain 'B' and resid 466 through 474
    Processing helix  chain 'B' and resid 475 through 478
      removed outlier: 6.598A  pdb=" N   LYS B 478 " --> pdb=" O   LEU B 475 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 475 through 478'
    Processing helix  chain 'B' and resid 479 through 486
    Processing helix  chain 'B' and resid 488 through 490
      No H-bonds generated for 'chain 'B' and resid 488 through 490'
    Processing helix  chain 'B' and resid 491 through 512
    Processing helix  chain 'B' and resid 540 through 562
      Proline residue:  B 546  - end of helix
      removed outlier: 3.909A  pdb=" N   PHE B 560 " --> pdb=" O   ILE B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 587
    Processing helix  chain 'B' and resid 598 through 624
    Processing helix  chain 'B' and resid 626 through 633
    Processing helix  chain 'B' and resid 634 through 651
      removed outlier: 3.565A  pdb=" N   VAL B 638 " --> pdb=" O   ILE B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 652 through 656
    Processing helix  chain 'B' and resid 659 through 674
      removed outlier: 3.670A  pdb=" N   ARG B 672 " --> pdb=" O   LYS B 668 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 675 through 684
      removed outlier: 4.083A  pdb=" N   SER B 681 " --> pdb=" O   SER B 677 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 224
      removed outlier: 3.897A  pdb=" N   SER A 222 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 220 through 224
      removed outlier: 3.897A  pdb=" N   SER B 222 " --> pdb=" O   SER B 307 " (cutoff:3.500A)

    583 hydrogen bonds defined for protein.
    1671 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.39

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1283
        1.30 -     1.43: 2361
        1.43 -     1.55: 4707
        1.55 -     1.67: 301
        1.67 -     1.80: 40
  Bond restraints: 8692
  Sorted by residual:
  bond pdb=" C10 CLR B 802 "
       pdb=" C9  CLR B 802 "
    ideal  model  delta    sigma   weight residual
    1.551  1.715 -0.164 2.00e-02 2.50e+03 6.73e+01
  bond pdb=" C10 CLR A 802 "
       pdb=" C9  CLR A 802 "
    ideal  model  delta    sigma   weight residual
    1.551  1.715 -0.164 2.00e-02 2.50e+03 6.73e+01
  bond pdb=" C4  CLR B 802 "
       pdb=" C5  CLR B 802 "
    ideal  model  delta    sigma   weight residual
    1.506  1.660 -0.154 2.00e-02 2.50e+03 5.94e+01
  bond pdb=" C4  CLR A 802 "
       pdb=" C5  CLR A 802 "
    ideal  model  delta    sigma   weight residual
    1.506  1.659 -0.153 2.00e-02 2.50e+03 5.87e+01
  bond pdb=" C10 CLR A 801 "
       pdb=" C9  CLR A 801 "
    ideal  model  delta    sigma   weight residual
    1.551  1.704 -0.153 2.00e-02 2.50e+03 5.87e+01
  ... (remaining 8687 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 10242
        2.36 -     4.73: 1324
        4.73 -     7.09: 184
        7.09 -     9.46: 28
        9.46 -    11.82: 2
  Bond angle restraints: 11780
  Sorted by residual:
  angle pdb=" C   SER B 562 "
        pdb=" N   PRO B 563 "
        pdb=" CA  PRO B 563 "
      ideal   model   delta    sigma   weight residual
     119.56  128.55   -8.99 1.02e+00 9.61e-01 7.77e+01
  angle pdb=" C   SER A 562 "
        pdb=" N   PRO A 563 "
        pdb=" CA  PRO A 563 "
      ideal   model   delta    sigma   weight residual
     119.56  128.53   -8.97 1.02e+00 9.61e-01 7.74e+01
  angle pdb=" C   TYR A 658 "
        pdb=" N   PRO A 659 "
        pdb=" CA  PRO A 659 "
      ideal   model   delta    sigma   weight residual
     120.21  127.68   -7.47 9.60e-01 1.09e+00 6.06e+01
  angle pdb=" C   TYR B 658 "
        pdb=" N   PRO B 659 "
        pdb=" CA  PRO B 659 "
      ideal   model   delta    sigma   weight residual
     120.21  127.65   -7.44 9.60e-01 1.09e+00 6.01e+01
  angle pdb=" C   LEU A 410 "
        pdb=" N   PRO A 411 "
        pdb=" CA  PRO A 411 "
      ideal   model   delta    sigma   weight residual
     119.82  127.26   -7.44 9.80e-01 1.04e+00 5.76e+01
  ... (remaining 11775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.82: 4982
       15.82 -    31.64: 250
       31.64 -    47.46: 46
       47.46 -    63.28: 34
       63.28 -    79.09: 4
  Dihedral angle restraints: 5316
    sinusoidal: 2338
      harmonic: 2978
  Sorted by residual:
  dihedral pdb=" N   LEU A 652 "
           pdb=" C   LEU A 652 "
           pdb=" CA  LEU A 652 "
           pdb=" CB  LEU A 652 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.22   -8.42     0      2.50e+00 1.60e-01 1.13e+01
  dihedral pdb=" N   LEU B 652 "
           pdb=" C   LEU B 652 "
           pdb=" CA  LEU B 652 "
           pdb=" CB  LEU B 652 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.16   -8.36     0      2.50e+00 1.60e-01 1.12e+01
  dihedral pdb=" C   TRP B 599 "
           pdb=" N   TRP B 599 "
           pdb=" CA  TRP B 599 "
           pdb=" CB  TRP B 599 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.71    8.11     0      2.50e+00 1.60e-01 1.05e+01
  ... (remaining 5313 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 912
       0.102 -    0.203: 338
       0.203 -    0.304: 80
       0.304 -    0.406: 16
       0.406 -    0.507: 16
  Chirality restraints: 1362
  Sorted by residual:
  chirality pdb=" CB  ILE B  26 "
            pdb=" CA  ILE B  26 "
            pdb=" CG1 ILE B  26 "
            pdb=" CG2 ILE B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    3.15   -0.51 2.00e-01 2.50e+01 6.43e+00
  chirality pdb=" CB  ILE A  26 "
            pdb=" CA  ILE A  26 "
            pdb=" CG1 ILE A  26 "
            pdb=" CG2 ILE A  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    3.15   -0.51 2.00e-01 2.50e+01 6.38e+00
  chirality pdb=" CB  ILE B 368 "
            pdb=" CA  ILE B 368 "
            pdb=" CG1 ILE B 368 "
            pdb=" CG2 ILE B 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    3.13   -0.49 2.00e-01 2.50e+01 5.97e+00
  ... (remaining 1359 not shown)

  Planarity restraints: 1398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  24 "   -0.052 2.00e-02 2.50e+03   3.15e-02 1.98e+01
        pdb=" CG  TYR B  24 "    0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  24 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  24 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  24 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  24 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  24 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B  24 "   -0.053 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  24 "    0.052 2.00e-02 2.50e+03   3.14e-02 1.97e+01
        pdb=" CG  TYR A  24 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  24 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  24 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  24 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  24 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  24 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A  24 "    0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 215 "   -0.059 2.00e-02 2.50e+03   2.98e-02 1.78e+01
        pdb=" CG  TYR B 215 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 215 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 215 "    0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 215 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 215 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 215 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 215 "   -0.037 2.00e-02 2.50e+03
  ... (remaining 1395 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 3280
        2.89 -     3.39: 8658
        3.39 -     3.89: 14173
        3.89 -     4.40: 18020
        4.40 -     4.90: 27840
  Nonbonded interactions: 71971
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A  75 "
            pdb=" NZ  LYS A 174 "
     model   vdw
     2.385 3.120
  nonbonded pdb=" OD1 ASP B  75 "
            pdb=" NZ  LYS B 174 "
     model   vdw
     2.385 3.120
  nonbonded pdb=" CB  GLU A 510 "
            pdb=" OE1 GLU A 510 "
     model   vdw
     2.412 2.752
  nonbonded pdb=" CB  GLU B 510 "
            pdb=" OE1 GLU B 510 "
     model   vdw
     2.412 2.752
  nonbonded pdb=" N   PRO A 335 "
            pdb=" O   PRO A 335 "
     model   vdw
     2.508 2.496
  ... (remaining 71966 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: 0.02
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.210
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
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      :  0.027   0.164   8692  Z= 1.382
  Angle     :  1.654  11.819  11780  Z= 1.110
  Chirality :  0.120   0.507   1362
  Planarity :  0.008   0.031   1398
  Dihedral  : 11.192  79.094   3380
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 1.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.25), residues: 984
  helix:  0.45 (0.18), residues: 706
  sheet:  2.58 (0.99), residues: 24
  loop :  0.92 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 470 
 TYR   0.059   0.009   TYR B 215 
 PHE   0.039   0.006   PHE A  99 
 TRP   0.035   0.007   TRP A 599 
 HIS   0.007   0.003   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.02659 ( 8692)
  covalent geometry    : angle       1.65415 (11780)
  hydrogen bonds       : bond        0.14387 (  583)
  hydrogen bonds       : angle       6.73068 ( 1671)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  426 MET cc_start: 0.8327 (mmt) cc_final: 0.7787 (mmt)
REVERT: B  426 MET cc_start: 0.8314 (mmt) cc_final: 0.7575 (mmt)
  outliers start: 0
  outliers final: 2
  residues processed: 151
  average time/residue: 0.4008
  time to fit residues: 65.3565
Evaluate side-chains
  68 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain B residue  109 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 223 HIS
A 543 GLN
B 223 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.126414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.103224 restraints weight = 13042.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.91
r_work: 0.3350 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8692  Z= 0.181
  Angle     :  0.633   6.066  11780  Z= 0.330
  Chirality :  0.046   0.155   1362
  Planarity :  0.005   0.040   1398
  Dihedral  :  9.757  58.102   1566
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  8.85 %
    Favored  : 89.38 %
  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 aren not related in a simple way.
  whole:  1.94 (0.26), residues: 984
  helix:  1.63 (0.19), residues: 694
  sheet:  1.33 (1.09), residues: 24
  loop :  0.55 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 650 
 TYR   0.021   0.002   TYR B 577 
 PHE   0.023   0.002   PHE A 415 
 TRP   0.016   0.002   TRP A 599 
 HIS   0.009   0.002   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 8692)
  covalent geometry    : angle       0.63315 (11780)
  hydrogen bonds       : bond        0.05673 (  583)
  hydrogen bonds       : angle       5.14952 ( 1671)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  132 ASP cc_start: 0.8290 (m-30) cc_final: 0.8027 (p0)
REVERT: A  145 LYS cc_start: 0.8015 (mptt) cc_final: 0.7558 (mmpt)
REVERT: A  174 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8514 (mtpp)
REVERT: A  198 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7805 (mm)
REVERT: A  688 ARG cc_start: 0.7477 (ttp80) cc_final: 0.7268 (ptm-80)
REVERT: B  145 LYS cc_start: 0.8056 (mptt) cc_final: 0.7645 (mmpt)
REVERT: B  174 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8500 (mtpp)
REVERT: B  202 ASN cc_start: 0.7836 (m-40) cc_final: 0.7619 (t0)
REVERT: B  426 MET cc_start: 0.7461 (mmt) cc_final: 0.7241 (mmt)
  outliers start: 16
  outliers final: 4
  residues processed: 93
  average time/residue: 0.4746
  time to fit residues: 47.7312
Evaluate side-chains
  69 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue  174 LYS
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  418 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0040
   chunk 54 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.6994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.127169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.104376 restraints weight = 12928.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.92
r_work: 0.3357 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8692  Z= 0.139
  Angle     :  0.540   5.626  11780  Z= 0.280
  Chirality :  0.043   0.134   1362
  Planarity :  0.005   0.043   1398
  Dihedral  :  8.967  59.395   1564
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  :  9.40 %
    Favored  : 87.72 %
  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 aren not related in a simple way.
  whole:  2.13 (0.26), residues: 984
  helix:  1.77 (0.19), residues: 696
  sheet:  1.44 (1.12), residues: 24
  loop :  0.61 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 688 
 TYR   0.014   0.002   TYR B 577 
 PHE   0.017   0.001   PHE A  99 
 TRP   0.020   0.002   TRP B 504 
 HIS   0.002   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8692)
  covalent geometry    : angle       0.54041 (11780)
  hydrogen bonds       : bond        0.04638 (  583)
  hydrogen bonds       : angle       4.71159 ( 1671)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  585 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6560 (mt)
REVERT: A  613 MET cc_start: 0.8711 (tmm) cc_final: 0.8496 (tmm)
REVERT: A  688 ARG cc_start: 0.7571 (ttp80) cc_final: 0.7354 (ptm-80)
REVERT: B  131 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7339 (ttt)
REVERT: B  145 LYS cc_start: 0.7994 (mptt) cc_final: 0.7655 (mmpt)
REVERT: B  426 MET cc_start: 0.7462 (mmt) cc_final: 0.7126 (mmt)
REVERT: B  468 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7626 (tm)
REVERT: B  585 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6164 (mt)
REVERT: B  613 MET cc_start: 0.8693 (tmm) cc_final: 0.8487 (tmm)
  outliers start: 26
  outliers final: 7
  residues processed: 101
  average time/residue: 0.3865
  time to fit residues: 42.8068
Evaluate side-chains
  81 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  644 SER
Chi-restraints excluded: chain B residue  688 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 543 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.124575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.101643 restraints weight = 13166.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.90
r_work: 0.3311 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8692  Z= 0.190
  Angle     :  0.584   9.065  11780  Z= 0.296
  Chirality :  0.045   0.146   1362
  Planarity :  0.005   0.046   1398
  Dihedral  :  9.167  59.809   1562
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 10.29 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.27), residues: 984
  helix:  1.64 (0.19), residues: 698
  sheet:  0.96 (1.13), residues: 24
  loop :  0.69 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 470 
 TYR   0.018   0.002   TYR B 170 
 PHE   0.023   0.002   PHE A 415 
 TRP   0.018   0.002   TRP B 504 
 HIS   0.003   0.001   HIS A 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8692)
  covalent geometry    : angle       0.58446 (11780)
  hydrogen bonds       : bond        0.04789 (  583)
  hydrogen bonds       : angle       4.77631 ( 1671)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  131 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7483 (ttt)
REVERT: A  585 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6741 (mt)
REVERT: A  670 ASP cc_start: 0.7633 (m-30) cc_final: 0.7041 (m-30)
REVERT: A  688 ARG cc_start: 0.7570 (ttp80) cc_final: 0.7368 (ptm-80)
REVERT: B  131 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7351 (ttt)
REVERT: B  585 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6412 (mt)
REVERT: B  670 ASP cc_start: 0.7641 (m-30) cc_final: 0.7407 (m-30)
  outliers start: 25
  outliers final: 13
  residues processed: 85
  average time/residue: 0.4086
  time to fit residues: 37.9434
Evaluate side-chains
  82 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain B residue  131 MET
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  418 PHE
Chi-restraints excluded: chain B residue  425 ILE
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  644 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 77 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0980
   chunk 67 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0070
   chunk 92 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.3798

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 543 GLN
B 543 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.127832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.105100 restraints weight = 13109.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.93
r_work: 0.3368 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8692  Z= 0.117
  Angle     :  0.512   7.373  11780  Z= 0.261
  Chirality :  0.041   0.131   1362
  Planarity :  0.005   0.048   1398
  Dihedral  :  8.664  59.331   1562
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 10.84 %
    Favored  : 86.62 %
  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 aren not related in a simple way.
  whole:  2.45 (0.27), residues: 984
  helix:  2.06 (0.20), residues: 686
  sheet:  0.91 (1.12), residues: 24
  loop :  0.71 (0.41), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 309 
 TYR   0.013   0.001   TYR A 170 
 PHE   0.015   0.001   PHE B  99 
 TRP   0.016   0.001   TRP A 504 
 HIS   0.002   0.000   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8692)
  covalent geometry    : angle       0.51232 (11780)
  hydrogen bonds       : bond        0.04156 (  583)
  hydrogen bonds       : angle       4.58336 ( 1671)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  145 LYS cc_start: 0.7781 (mmpt) cc_final: 0.7443 (mmpt)
REVERT: A  585 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6547 (mt)
REVERT: A  657 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8741 (p)
REVERT: A  670 ASP cc_start: 0.7527 (m-30) cc_final: 0.7288 (m-30)
REVERT: A  688 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7332 (ptm-80)
REVERT: B  426 MET cc_start: 0.7467 (mmt) cc_final: 0.7147 (mmt)
REVERT: B  468 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7706 (tm)
REVERT: B  585 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6418 (mt)
REVERT: B  670 ASP cc_start: 0.7447 (m-30) cc_final: 0.7219 (m-30)
  outliers start: 23
  outliers final: 5
  residues processed: 96
  average time/residue: 0.3265
  time to fit residues: 34.5272
Evaluate side-chains
  84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  644 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 95 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 543 GLN
B 543 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.126375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.103367 restraints weight = 12939.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.89
r_work: 0.3342 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8692  Z= 0.147
  Angle     :  0.544   9.512  11780  Z= 0.273
  Chirality :  0.043   0.134   1362
  Planarity :  0.005   0.051   1398
  Dihedral  :  8.774  58.842   1562
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.39 %
    Favored  : 86.39 %
  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 aren not related in a simple way.
  whole:  2.31 (0.27), residues: 984
  helix:  1.99 (0.19), residues: 686
  sheet: -0.30 (0.99), residues: 30
  loop :  0.70 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 470 
 TYR   0.013   0.002   TYR B 577 
 PHE   0.022   0.002   PHE B 415 
 TRP   0.017   0.001   TRP A 504 
 HIS   0.002   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8692)
  covalent geometry    : angle       0.54445 (11780)
  hydrogen bonds       : bond        0.04386 (  583)
  hydrogen bonds       : angle       4.62112 ( 1671)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  561 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8168 (mm)
REVERT: A  585 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6632 (mt)
REVERT: A  670 ASP cc_start: 0.7592 (m-30) cc_final: 0.6935 (m-30)
REVERT: A  688 ARG cc_start: 0.7559 (ttp80) cc_final: 0.7348 (ptm-80)
REVERT: B  145 LYS cc_start: 0.7816 (mmpt) cc_final: 0.7487 (mmpt)
REVERT: B  426 MET cc_start: 0.7501 (mmt) cc_final: 0.7243 (mmt)
REVERT: B  468 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7699 (tm)
REVERT: B  474 PHE cc_start: 0.7781 (m-80) cc_final: 0.7492 (m-10)
REVERT: B  561 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8173 (mm)
REVERT: B  585 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6365 (mt)
REVERT: B  670 ASP cc_start: 0.7464 (m-30) cc_final: 0.7183 (m-30)
  outliers start: 20
  outliers final: 6
  residues processed: 92
  average time/residue: 0.3740
  time to fit residues: 37.8116
Evaluate side-chains
  84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  644 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0570
   chunk 80 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0370
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 543 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.126827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.103712 restraints weight = 13047.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.91
r_work: 0.3349 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8692  Z= 0.134
  Angle     :  0.537  10.072  11780  Z= 0.270
  Chirality :  0.042   0.143   1362
  Planarity :  0.005   0.055   1398
  Dihedral  :  8.686  59.621   1562
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.50 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.27), residues: 984
  helix:  2.03 (0.19), residues: 686
  sheet: -0.39 (0.99), residues: 30
  loop :  0.70 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 470 
 TYR   0.014   0.002   TYR A 469 
 PHE   0.017   0.001   PHE B  99 
 TRP   0.017   0.001   TRP A 504 
 HIS   0.002   0.001   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8692)
  covalent geometry    : angle       0.53729 (11780)
  hydrogen bonds       : bond        0.04242 (  583)
  hydrogen bonds       : angle       4.58232 ( 1671)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  474 PHE cc_start: 0.7774 (m-80) cc_final: 0.7525 (m-10)
REVERT: A  561 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8143 (mm)
REVERT: A  585 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6565 (mt)
REVERT: A  670 ASP cc_start: 0.7508 (m-30) cc_final: 0.6868 (m-30)
REVERT: A  688 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7293 (ptm-80)
REVERT: B  468 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7678 (tm)
REVERT: B  474 PHE cc_start: 0.7779 (m-80) cc_final: 0.7512 (m-10)
REVERT: B  561 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8127 (mm)
REVERT: B  585 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6405 (mt)
  outliers start: 23
  outliers final: 8
  residues processed: 95
  average time/residue: 0.3870
  time to fit residues: 40.0342
Evaluate side-chains
  88 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  504 TRP
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  504 TRP
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  644 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 543 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.123898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.100673 restraints weight = 12892.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.89
r_work: 0.3313 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8692  Z= 0.186
  Angle     :  0.582   9.589  11780  Z= 0.292
  Chirality :  0.045   0.195   1362
  Planarity :  0.005   0.055   1398
  Dihedral  :  9.024  59.810   1562
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.50 %
    Favored  : 85.62 %
  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 aren not related in a simple way.
  whole:  2.02 (0.27), residues: 984
  helix:  1.80 (0.19), residues: 684
  sheet: -0.68 (1.01), residues: 30
  loop :  0.57 (0.41), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 470 
 TYR   0.014   0.002   TYR B 577 
 PHE   0.022   0.002   PHE B 415 
 TRP   0.018   0.002   TRP A 504 
 HIS   0.002   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 8692)
  covalent geometry    : angle       0.58187 (11780)
  hydrogen bonds       : bond        0.04558 (  583)
  hydrogen bonds       : angle       4.71746 ( 1671)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  474 PHE cc_start: 0.7727 (m-80) cc_final: 0.7491 (m-10)
REVERT: A  561 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8149 (mm)
REVERT: A  585 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6615 (mt)
REVERT: A  670 ASP cc_start: 0.7673 (m-30) cc_final: 0.7005 (m-30)
REVERT: A  688 ARG cc_start: 0.7558 (ttp80) cc_final: 0.7348 (ptm-80)
REVERT: B  426 MET cc_start: 0.7471 (mmt) cc_final: 0.7228 (mmt)
REVERT: B  468 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7699 (tm)
REVERT: B  474 PHE cc_start: 0.7710 (m-80) cc_final: 0.7472 (m-10)
REVERT: B  561 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8148 (mm)
REVERT: B  585 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6609 (mt)
REVERT: B  670 ASP cc_start: 0.7437 (m-30) cc_final: 0.7125 (m-30)
  outliers start: 17
  outliers final: 10
  residues processed: 84
  average time/residue: 0.3770
  time to fit residues: 34.7949
Evaluate side-chains
  81 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  425 ILE
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  504 TRP
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  644 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 83 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0570
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 543 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.126199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.103195 restraints weight = 12945.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.89
r_work: 0.3350 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8692  Z= 0.126
  Angle     :  0.531   9.511  11780  Z= 0.267
  Chirality :  0.042   0.203   1362
  Planarity :  0.005   0.056   1398
  Dihedral  :  8.728  59.172   1562
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.05 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.27), residues: 984
  helix:  2.01 (0.19), residues: 686
  sheet: -0.45 (0.99), residues: 30
  loop :  0.67 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 688 
 TYR   0.011   0.001   TYR A 572 
 PHE   0.017   0.001   PHE B  99 
 TRP   0.019   0.001   TRP A 504 
 HIS   0.002   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8692)
  covalent geometry    : angle       0.53104 (11780)
  hydrogen bonds       : bond        0.04147 (  583)
  hydrogen bonds       : angle       4.57603 ( 1671)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A  426 MET cc_start: 0.7440 (mmt) cc_final: 0.7155 (mmt)
REVERT: A  561 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8002 (mm)
REVERT: A  670 ASP cc_start: 0.7548 (m-30) cc_final: 0.6894 (m-30)
REVERT: A  688 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7152 (ptm-80)
REVERT: B  426 MET cc_start: 0.7423 (mmt) cc_final: 0.7051 (mmt)
REVERT: B  468 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7648 (tm)
REVERT: B  474 PHE cc_start: 0.7697 (m-80) cc_final: 0.7465 (m-10)
REVERT: B  561 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7989 (mm)
  outliers start: 17
  outliers final: 8
  residues processed: 87
  average time/residue: 0.4042
  time to fit residues: 38.3807
Evaluate side-chains
  83 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  504 TRP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  504 TRP
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  644 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0970
   chunk 95 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0570
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.127624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.104695 restraints weight = 12948.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.91
r_work: 0.3364 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8692  Z= 0.118
  Angle     :  0.539  10.027  11780  Z= 0.268
  Chirality :  0.043   0.248   1362
  Planarity :  0.005   0.058   1398
  Dihedral  :  8.525  58.385   1562
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.50 %
    Favored  : 84.73 %
  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 aren not related in a simple way.
  whole:  2.35 (0.27), residues: 984
  helix:  2.10 (0.20), residues: 686
  sheet: -0.68 (0.82), residues: 40
  loop :  0.59 (0.42), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 672 
 TYR   0.017   0.002   TYR A 469 
 PHE   0.029   0.001   PHE A 415 
 TRP   0.018   0.001   TRP A 504 
 HIS   0.001   0.000   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8692)
  covalent geometry    : angle       0.53918 (11780)
  hydrogen bonds       : bond        0.04085 (  583)
  hydrogen bonds       : angle       4.53641 ( 1671)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  426 MET cc_start: 0.7560 (mmt) cc_final: 0.7125 (mmt)
REVERT: A  561 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8080 (mm)
REVERT: A  670 ASP cc_start: 0.7545 (m-30) cc_final: 0.6904 (m-30)
REVERT: B  468 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7651 (tm)
REVERT: B  474 PHE cc_start: 0.7669 (m-80) cc_final: 0.7393 (m-10)
REVERT: B  561 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8074 (mm)
  outliers start: 16
  outliers final: 9
  residues processed: 89
  average time/residue: 0.3955
  time to fit residues: 38.1744
Evaluate side-chains
  85 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  504 TRP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  504 TRP
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  644 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 57 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 23 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.126570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.103600 restraints weight = 12908.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.90
r_work: 0.3346 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8692  Z= 0.135
  Angle     :  0.549   9.637  11780  Z= 0.275
  Chirality :  0.043   0.249   1362
  Planarity :  0.005   0.059   1398
  Dihedral  :  8.616  57.843   1562
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 13.94 %
    Favored  : 84.85 %
  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 aren not related in a simple way.
  whole:  2.31 (0.27), residues: 984
  helix:  2.05 (0.19), residues: 686
  sheet: -0.59 (1.00), residues: 30
  loop :  0.56 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 688 
 TYR   0.015   0.001   TYR A 687 
 PHE   0.018   0.001   PHE B  99 
 TRP   0.018   0.001   TRP A 504 
 HIS   0.002   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8692)
  covalent geometry    : angle       0.54873 (11780)
  hydrogen bonds       : bond        0.04204 (  583)
  hydrogen bonds       : angle       4.56671 ( 1671)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2783.45 seconds
wall clock time: 48 minutes 13.09 seconds (2893.09 seconds total)