Starting phenix.real_space_refine
on Mon May 12 02:52:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t57_41044/05_2025/8t57_41044.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t57_41044/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t57_41044/05_2025/8t57_41044.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t57_41044/05_2025/8t57_41044.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t57_41044/05_2025/8t57_41044.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t57_41044/05_2025/8t57_41044.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.84, per 1000 atoms: 0.93
  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: 2.58
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.94
  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: 2.53

  Time building geometry restraints manager: 2.94 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: 0.04
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:             0.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.480
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:10.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.180
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.035   0.007   TRP A 599 
 HIS   0.007   0.003   HIS A 614 
 PHE   0.039   0.006   PHE A  99 
 TYR   0.059   0.009   TYR B 215 
 ARG   0.005   0.001   ARG B 470 

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

*********************** 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  : 1.038 
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: 0.9344
  time to fit residues: 153.0208
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  : 0.943 
-------------------------------------------------------------------------------
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 84 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.124971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.101755 restraints weight = 12896.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 1.89
r_work: 0.3331 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   8692  Z= 0.204
  Angle     :  0.650   6.919  11780  Z= 0.336
  Chirality :  0.047   0.173   1362
  Planarity :  0.005   0.040   1398
  Dihedral  :  9.913  56.812   1566
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  8.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.26), residues: 984
  helix:  1.53 (0.19), residues: 694
  sheet:  1.32 (1.09), residues: 24
  loop :  0.44 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 599 
 HIS   0.008   0.002   HIS A 223 
 PHE   0.023   0.002   PHE A 415 
 TYR   0.019   0.002   TYR B 577 
 ARG   0.002   0.000   ARG B 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05690 (  583)
  hydrogen bonds       : angle       5.17781 ( 1671)
  covalent geometry    : bond        0.00488 ( 8692)
  covalent geometry    : angle       0.64973 (11780)

*********************** 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
  108 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A  132 ASP cc_start: 0.8317 (m-30) cc_final: 0.8077 (p0)
REVERT: A  145 LYS cc_start: 0.8019 (mptt) cc_final: 0.7744 (mmpt)
REVERT: A  174 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8522 (mtpp)
REVERT: B  174 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8497 (mtpp)
  outliers start: 23
  outliers final: 9
  residues processed: 96
  average time/residue: 0.8818
  time to fit residues: 92.5399
Evaluate side-chains
  74 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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  218 SER
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  174 LYS
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  418 PHE
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  644 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.125968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.103007 restraints weight = 13125.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.92
r_work: 0.3341 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8692  Z= 0.153
  Angle     :  0.555   5.331  11780  Z= 0.288
  Chirality :  0.044   0.137   1362
  Planarity :  0.005   0.042   1398
  Dihedral  :  9.199  59.062   1566
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  :  9.40 %
    Favored  : 87.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.26), residues: 984
  helix:  1.67 (0.19), residues: 696
  sheet:  1.28 (1.10), residues: 24
  loop :  0.57 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 504 
 HIS   0.002   0.001   HIS A 149 
 PHE   0.018   0.001   PHE A  99 
 TYR   0.014   0.002   TYR B 577 
 ARG   0.001   0.000   ARG A 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04811 (  583)
  hydrogen bonds       : angle       4.79063 ( 1671)
  covalent geometry    : bond        0.00353 ( 8692)
  covalent geometry    : angle       0.55472 (11780)

*********************** 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
  112 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 82
  time to evaluate  : 1.019 
Fit side-chains
REVERT: A  145 LYS cc_start: 0.7994 (mptt) cc_final: 0.7783 (mmpt)
REVERT: A  543 GLN cc_start: 0.8173 (mt0) cc_final: 0.7927 (tm-30)
REVERT: B  131 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7331 (ttt)
REVERT: B  145 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7716 (mmpt)
REVERT: B  468 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7668 (tm)
REVERT: B  474 PHE cc_start: 0.7871 (m-80) cc_final: 0.7583 (m-80)
REVERT: B  585 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6320 (mt)
  outliers start: 30
  outliers final: 15
  residues processed: 102
  average time/residue: 0.8755
  time to fit residues: 97.7140
Evaluate side-chains
  85 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  688 ARG
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  418 PHE
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  508 SER
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  644 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    0.4980
   chunk 34 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   chunk 98 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.126215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.103389 restraints weight = 13042.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 1.92
r_work: 0.3345 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2913

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= 0.139
  Angle     :  0.546   8.890  11780  Z= 0.276
  Chirality :  0.043   0.136   1362
  Planarity :  0.005   0.046   1398
  Dihedral  :  8.914  59.651   1562
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 10.18 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.27), residues: 984
  helix:  1.78 (0.19), residues: 698
  sheet:  1.31 (1.11), residues: 24
  loop :  0.70 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 504 
 HIS   0.002   0.001   HIS B 168 
 PHE   0.026   0.001   PHE A 415 
 TYR   0.018   0.002   TYR B 170 
 ARG   0.002   0.000   ARG A 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04494 (  583)
  hydrogen bonds       : angle       4.69600 ( 1671)
  covalent geometry    : bond        0.00316 ( 8692)
  covalent geometry    : angle       0.54603 (11780)

*********************** 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
  102 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A  131 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7424 (ttt)
REVERT: A  560 PHE cc_start: 0.8849 (t80) cc_final: 0.8590 (t80)
REVERT: A  657 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8713 (p)
REVERT: A  670 ASP cc_start: 0.7618 (m-30) cc_final: 0.7071 (m-30)
REVERT: B  543 GLN cc_start: 0.8143 (mp10) cc_final: 0.7933 (tm-30)
REVERT: B  585 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6397 (mt)
REVERT: B  670 ASP cc_start: 0.7678 (m-30) cc_final: 0.7244 (m-30)
  outliers start: 24
  outliers final: 12
  residues processed: 92
  average time/residue: 0.8172
  time to fit residues: 82.9075
Evaluate side-chains
  86 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
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  425 ILE
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  657 SER
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  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 74 optimal weight:    7.9990
   chunk 7 optimal weight:    0.3980
   chunk 6 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 81 optimal weight:    0.3980
   chunk 75 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   chunk 86 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.127382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.104400 restraints weight = 12962.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.90
r_work: 0.3365 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8692  Z= 0.127
  Angle     :  0.527   8.064  11780  Z= 0.266
  Chirality :  0.042   0.130   1362
  Planarity :  0.005   0.047   1398
  Dihedral  :  8.747  59.067   1562
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 10.51 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.27), residues: 984
  helix:  2.02 (0.19), residues: 686
  sheet:  1.06 (1.10), residues: 24
  loop :  0.65 (0.41), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 504 
 HIS   0.002   0.000   HIS B 168 
 PHE   0.016   0.001   PHE A  99 
 TYR   0.013   0.002   TYR A 170 
 ARG   0.002   0.000   ARG A 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04290 (  583)
  hydrogen bonds       : angle       4.61131 ( 1671)
  covalent geometry    : bond        0.00290 ( 8692)
  covalent geometry    : angle       0.52668 (11780)

*********************** 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: 24
    poor density    : 81
  time to evaluate  : 0.949 
Fit side-chains
REVERT: A  560 PHE cc_start: 0.8841 (t80) cc_final: 0.8593 (t80)
REVERT: A  657 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8722 (p)
REVERT: A  670 ASP cc_start: 0.7555 (m-30) cc_final: 0.6981 (m-30)
REVERT: B  426 MET cc_start: 0.7472 (mmt) cc_final: 0.7157 (mmt)
REVERT: B  468 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7659 (tm)
REVERT: B  585 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6438 (mt)
REVERT: B  670 ASP cc_start: 0.7517 (m-30) cc_final: 0.6993 (m-30)
  outliers start: 24
  outliers final: 8
  residues processed: 95
  average time/residue: 0.8200
  time to fit residues: 85.7144
Evaluate side-chains
  85 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  418 PHE
Chi-restraints excluded: chain B residue  457 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 81 optimal weight:    0.4980
   chunk 2 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 24 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.125787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.103062 restraints weight = 12831.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.87
r_work: 0.3336 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8692  Z= 0.153
  Angle     :  0.548   9.354  11780  Z= 0.276
  Chirality :  0.043   0.142   1362
  Planarity :  0.005   0.050   1398
  Dihedral  :  8.878  58.159   1562
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 10.84 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.27), residues: 984
  helix:  1.95 (0.19), residues: 686
  sheet: -0.27 (0.98), residues: 30
  loop :  0.69 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 504 
 HIS   0.002   0.001   HIS A 168 
 PHE   0.025   0.002   PHE B 415 
 TYR   0.014   0.002   TYR A 469 
 ARG   0.002   0.000   ARG B 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04417 (  583)
  hydrogen bonds       : angle       4.63888 ( 1671)
  covalent geometry    : bond        0.00366 ( 8692)
  covalent geometry    : angle       0.54794 (11780)

*********************** 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
  97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A  474 PHE cc_start: 0.7805 (m-80) cc_final: 0.7511 (m-10)
REVERT: A  561 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8081 (mm)
REVERT: A  585 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6612 (mt)
REVERT: A  670 ASP cc_start: 0.7601 (m-30) cc_final: 0.6950 (m-30)
REVERT: B  145 LYS cc_start: 0.7842 (mmpt) cc_final: 0.7594 (mmpt)
REVERT: B  426 MET cc_start: 0.7537 (mmt) cc_final: 0.7239 (mmt)
REVERT: B  468 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7727 (tm)
REVERT: B  474 PHE cc_start: 0.7776 (m-80) cc_final: 0.7488 (m-10)
REVERT: B  585 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6392 (mt)
REVERT: B  670 ASP cc_start: 0.7591 (m-30) cc_final: 0.7047 (m-30)
  outliers start: 25
  outliers final: 8
  residues processed: 91
  average time/residue: 0.7748
  time to fit residues: 78.1599
Evaluate side-chains
  84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  218 SER
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  198 LEU
Chi-restraints excluded: chain B residue  218 SER
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  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 7 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0870
   chunk 47 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.1964

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.125375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.102543 restraints weight = 12974.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.88
r_work: 0.3331 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.3281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8692  Z= 0.160
  Angle     :  0.560  10.102  11780  Z= 0.283
  Chirality :  0.044   0.191   1362
  Planarity :  0.005   0.053   1398
  Dihedral  :  8.946  59.793   1562
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 10.95 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.27), residues: 984
  helix:  1.85 (0.19), residues: 686
  sheet: -0.56 (0.99), residues: 30
  loop :  0.65 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 504 
 HIS   0.002   0.001   HIS B 168 
 PHE   0.020   0.002   PHE A  99 
 TYR   0.013   0.002   TYR A 577 
 ARG   0.002   0.000   ARG B 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 (  583)
  hydrogen bonds       : angle       4.68407 ( 1671)
  covalent geometry    : bond        0.00384 ( 8692)
  covalent geometry    : angle       0.55997 (11780)

*********************** 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
  98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A  131 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7429 (ttt)
REVERT: A  145 LYS cc_start: 0.7836 (mmpt) cc_final: 0.7553 (mmpt)
REVERT: A  474 PHE cc_start: 0.7709 (m-80) cc_final: 0.7464 (m-10)
REVERT: A  670 ASP cc_start: 0.7584 (m-30) cc_final: 0.6952 (m-30)
REVERT: B  426 MET cc_start: 0.7446 (mmt) cc_final: 0.7127 (mmt)
REVERT: B  468 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7695 (tm)
REVERT: B  474 PHE cc_start: 0.7714 (m-80) cc_final: 0.7448 (m-10)
REVERT: B  561 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8168 (mm)
REVERT: B  585 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6534 (mt)
REVERT: B  670 ASP cc_start: 0.7582 (m-30) cc_final: 0.7025 (m-30)
  outliers start: 26
  outliers final: 11
  residues processed: 92
  average time/residue: 0.7610
  time to fit residues: 77.9609
Evaluate side-chains
  85 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
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  425 ILE
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  504 TRP
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 SER
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 16 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3827 r_free = 0.3827 target = 0.126576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.103738 restraints weight = 13055.822|
|-----------------------------------------------------------------------------|
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: 0.3199 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3389

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= 0.131
  Angle     :  0.544   9.714  11780  Z= 0.271
  Chirality :  0.043   0.262   1362
  Planarity :  0.005   0.055   1398
  Dihedral  :  8.776  59.855   1562
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.84 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.27), residues: 984
  helix:  1.94 (0.19), residues: 686
  sheet: -0.44 (1.00), residues: 30
  loop :  0.72 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 504 
 HIS   0.002   0.001   HIS B 168 
 PHE   0.025   0.001   PHE A 415 
 TYR   0.015   0.002   TYR A 469 
 ARG   0.002   0.000   ARG B 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04216 (  583)
  hydrogen bonds       : angle       4.62762 ( 1671)
  covalent geometry    : bond        0.00300 ( 8692)
  covalent geometry    : angle       0.54403 (11780)

*********************** 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
  100 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A  426 MET cc_start: 0.7516 (mmt) cc_final: 0.7196 (mmt)
REVERT: A  474 PHE cc_start: 0.7708 (m-80) cc_final: 0.7442 (m-10)
REVERT: A  561 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8151 (mm)
REVERT: A  585 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6541 (mt)
REVERT: A  670 ASP cc_start: 0.7574 (m-30) cc_final: 0.6913 (m-30)
REVERT: B  145 LYS cc_start: 0.7834 (mmpt) cc_final: 0.7593 (mmpt)
REVERT: B  468 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7712 (tm)
REVERT: B  474 PHE cc_start: 0.7699 (m-80) cc_final: 0.7411 (m-10)
REVERT: B  561 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8078 (mm)
REVERT: B  670 ASP cc_start: 0.7558 (m-30) cc_final: 0.6993 (m-30)
  outliers start: 22
  outliers final: 12
  residues processed: 93
  average time/residue: 0.8246
  time to fit residues: 84.5490
Evaluate side-chains
  85 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  425 ILE
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 A residue  585 LEU
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 SER
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   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**
A 543 GLN
** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 543 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.126277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.103231 restraints weight = 13006.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.91
r_work: 0.3343 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8692  Z= 0.136
  Angle     :  0.548   9.519  11780  Z= 0.275
  Chirality :  0.043   0.216   1362
  Planarity :  0.005   0.056   1398
  Dihedral  :  8.757  59.125   1562
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 12.50 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.27), residues: 984
  helix:  1.95 (0.19), residues: 686
  sheet: -0.57 (1.00), residues: 30
  loop :  0.67 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 504 
 HIS   0.002   0.001   HIS B 223 
 PHE   0.018   0.001   PHE A  99 
 TYR   0.012   0.001   TYR B 577 
 ARG   0.002   0.000   ARG A 688 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04257 (  583)
  hydrogen bonds       : angle       4.60985 ( 1671)
  covalent geometry    : bond        0.00317 ( 8692)
  covalent geometry    : angle       0.54828 (11780)

*********************** 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
  94 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A  426 MET cc_start: 0.7592 (mmt) cc_final: 0.7214 (mmt)
REVERT: A  474 PHE cc_start: 0.7693 (m-80) cc_final: 0.7421 (m-10)
REVERT: A  561 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8130 (mm)
REVERT: A  585 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6488 (mt)
REVERT: A  670 ASP cc_start: 0.7604 (m-30) cc_final: 0.6931 (m-30)
REVERT: B  145 LYS cc_start: 0.7794 (mmpt) cc_final: 0.7533 (mmpt)
REVERT: B  468 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7695 (tm)
REVERT: B  474 PHE cc_start: 0.7676 (m-80) cc_final: 0.7443 (m-10)
REVERT: B  561 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8159 (mm)
REVERT: B  670 ASP cc_start: 0.7572 (m-30) cc_final: 0.6993 (m-30)
  outliers start: 21
  outliers final: 9
  residues processed: 88
  average time/residue: 0.9280
  time to fit residues: 89.1799
Evaluate side-chains
  84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  218 SER
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 A residue  585 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 SER
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 75 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.126391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.103354 restraints weight = 12930.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.90
r_work: 0.3343 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   8692  Z= 0.138
  Angle     :  0.548   9.625  11780  Z= 0.275
  Chirality :  0.043   0.206   1362
  Planarity :  0.005   0.056   1398
  Dihedral  :  8.741  58.523   1562
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.38 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.27), residues: 984
  helix:  1.97 (0.19), residues: 686
  sheet: -0.59 (1.00), residues: 30
  loop :  0.61 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 504 
 HIS   0.002   0.001   HIS B 168 
 PHE   0.023   0.001   PHE A 415 
 TYR   0.012   0.001   TYR B 577 
 ARG   0.002   0.000   ARG B 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04303 (  583)
  hydrogen bonds       : angle       4.60527 ( 1671)
  covalent geometry    : bond        0.00331 ( 8692)
  covalent geometry    : angle       0.54769 (11780)

********************** 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
  88 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A  426 MET cc_start: 0.7590 (mmt) cc_final: 0.7183 (mmt)
REVERT: A  474 PHE cc_start: 0.7667 (m-80) cc_final: 0.7423 (m-10)
REVERT: A  561 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8120 (mm)
REVERT: A  585 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6478 (mt)
REVERT: A  670 ASP cc_start: 0.7586 (m-30) cc_final: 0.6924 (m-30)
REVERT: B  145 LYS cc_start: 0.7782 (mmpt) cc_final: 0.7582 (mmpt)
REVERT: B  426 MET cc_start: 0.7558 (mmt) cc_final: 0.7211 (mmt)
REVERT: B  468 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7711 (tm)
REVERT: B  474 PHE cc_start: 0.7686 (m-80) cc_final: 0.7448 (m-10)
REVERT: B  670 ASP cc_start: 0.7556 (m-30) cc_final: 0.6967 (m-30)
  outliers start: 15
  outliers final: 10
  residues processed: 85
  average time/residue: 0.8575
  time to fit residues: 80.0639
Evaluate side-chains
  84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  218 SER
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 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  218 SER
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  644 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.126760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.103754 restraints weight = 13056.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.92
r_work: 0.3349 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8692  Z= 0.132
  Angle     :  0.545   9.543  11780  Z= 0.275
  Chirality :  0.043   0.191   1362
  Planarity :  0.005   0.059   1398
  Dihedral  :  8.698  59.366   1562
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 13.50 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.27), residues: 984
  helix:  2.02 (0.19), residues: 686
  sheet: -0.61 (1.01), residues: 30
  loop :  0.56 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 504 
 HIS   0.002   0.001   HIS B 168 
 PHE   0.017   0.001   PHE A  99 
 TYR   0.018   0.002   TYR B 469 
 ARG   0.002   0.000   ARG B 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  583)
  hydrogen bonds       : angle       4.60091 ( 1671)
  covalent geometry    : bond        0.00307 ( 8692)
  covalent geometry    : angle       0.54535 (11780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5869.16 seconds
wall clock time: 102 minutes 2.32 seconds (6122.32 seconds total)