Starting phenix.real_space_refine
on Fri Aug 22 14:59:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tm1_41374/08_2025/8tm1_41374.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tm1_41374/08_2025/8tm1_41374.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tm1_41374/08_2025/8tm1_41374.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tm1_41374/08_2025/8tm1_41374.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tm1_41374/08_2025/8tm1_41374.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tm1_41374/08_2025/8tm1_41374.cif"
  }
  resolution = 2.79
  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=  -0.008 sd=   0.167
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      15      5.16       5
     C    2908      2.51       5
     N     754      2.21       5
     O     859      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  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: 4536
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1407
          Classifications: {'peptide': 175}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 166}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 1282
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1282
          Classifications: {'peptide': 159}
          Link IDs: {'PTRANS': 7, 'TRANS': 151}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 1015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1015
          Classifications: {'peptide': 127}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 120}
    Chain: "L"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 832
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 1.34, per 1000 atoms: 0.30
  Number of scatterers: 4536
  At special positions: 0
  Unit cell: (96.8, 74.8, 92.4, 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      15     16.00
     O     859      8.00
     N     754      7.00
     C    2908      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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: 0.36
  Conformation dependent library (CDL) restraints added in 211.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1044

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 12 sheets defined
      14.8% alpha, 32.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.528A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 4.450A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.408A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'B' and resid 339 through 343
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.653A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 371
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.074A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 505
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.703A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 356 through 357
    Processing sheet with id=AA4, first strand: chain 'B' and resid 376 through 379
      removed outlier: 3.522A  pdb=" N   PHE B 400 " --> pdb=" O   VAL B 510 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.715A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER H  70 " --> pdb=" O   SER H  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.500A  pdb=" N   VAL H 109 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA H  88 " --> pdb=" O   VAL H 109 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.909A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ASN H  50 " --> pdb=" O   TRP H  35A" (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   TRP H  35A" --> pdb=" O   ASN H  50 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   TYR H  52 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
      removed outlier: 8.953A  pdb=" N   TYR H  34 " --> pdb=" O   TYR H  52 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR H  35 " --> pdb=" O   GLY H  95 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ARG H  94 " --> pdb=" O   ILE H 102 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ILE H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.516A  pdb=" N   SER L   7 " --> pdb=" O   THR L  22 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  75 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   THR L  69 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 10.386A  pdb=" N   GLN L  27 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 10.177A  pdb=" N   SER L  67 " --> pdb=" O   GLN L  27 " (cutoff:3.500A)
      removed outlier: 12.189A  pdb=" N   ILE L  29 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
      removed outlier: 12.128A  pdb=" N   SER L  65 " --> pdb=" O   ILE L  29 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.675A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.812A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)

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

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1430
        1.34 -     1.47: 1322
        1.47 -     1.59: 1896
        1.59 -     1.71: 0
        1.71 -     1.83: 17
  Bond restraints: 4665
  Sorted by residual:
  bond pdb=" CB  PRO A 337 "
       pdb=" CG  PRO A 337 "
    ideal  model  delta    sigma   weight residual
    1.492  1.539 -0.047 5.00e-02 4.00e+02 8.83e-01
  bond pdb=" CB  MET L   4 "
       pdb=" CG  MET L   4 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 8.31e-01
  bond pdb=" SD  MET L   4 "
       pdb=" CE  MET L   4 "
    ideal  model  delta    sigma   weight residual
    1.791  1.769  0.022 2.50e-02 1.60e+03 7.51e-01
  bond pdb=" N   ASN H  65 "
       pdb=" CA  ASN H  65 "
    ideal  model  delta    sigma   weight residual
    1.460  1.472 -0.012 1.54e-02 4.22e+03 5.98e-01
  bond pdb=" N   SER H  54 "
       pdb=" CA  SER H  54 "
    ideal  model  delta    sigma   weight residual
    1.460  1.474 -0.015 1.95e-02 2.63e+03 5.86e-01
  ... (remaining 4660 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 6047
        1.47 -     2.94: 251
        2.94 -     4.41: 37
        4.41 -     5.88: 3
        5.88 -     7.35: 3
  Bond angle restraints: 6341
  Sorted by residual:
  angle pdb=" C   ASN H  64 "
        pdb=" N   ASN H  65 "
        pdb=" CA  ASN H  65 "
      ideal   model   delta    sigma   weight residual
     122.46  126.03   -3.57 1.41e+00 5.03e-01 6.42e+00
  angle pdb=" C   ASP L  50 "
        pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
      ideal   model   delta    sigma   weight residual
     121.54  126.32   -4.78 1.91e+00 2.74e-01 6.27e+00
  angle pdb=" CB  MET L   4 "
        pdb=" CG  MET L   4 "
        pdb=" SD  MET L   4 "
      ideal   model   delta    sigma   weight residual
     112.70  105.35    7.35 3.00e+00 1.11e-01 6.01e+00
  angle pdb=" C   ASN B 354 "
        pdb=" N   ARG B 355 "
        pdb=" CA  ARG B 355 "
      ideal   model   delta    sigma   weight residual
     122.81  126.20   -3.39 1.57e+00 4.06e-01 4.65e+00
  angle pdb=" N   ASN B 370 "
        pdb=" CA  ASN B 370 "
        pdb=" C   ASN B 370 "
      ideal   model   delta    sigma   weight residual
     112.23  114.67   -2.44 1.26e+00 6.30e-01 3.74e+00
  ... (remaining 6336 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 2475
       16.90 -    33.81: 193
       33.81 -    50.71: 24
       50.71 -    67.61: 5
       67.61 -    84.51: 6
  Dihedral angle restraints: 2703
    sinusoidal: 1053
      harmonic: 1650
  Sorted by residual:
  dihedral pdb=" CD  ARG B 457 "
           pdb=" NE  ARG B 457 "
           pdb=" CZ  ARG B 457 "
           pdb=" NH1 ARG B 457 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -35.01   35.01     1      1.00e+01 1.00e-02 1.74e+01
  dihedral pdb=" CG  ARG B 403 "
           pdb=" CD  ARG B 403 "
           pdb=" NE  ARG B 403 "
           pdb=" CZ  ARG B 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.71  -44.71     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CD  ARG A 408 "
           pdb=" NE  ARG A 408 "
           pdb=" CZ  ARG A 408 "
           pdb=" NH1 ARG A 408 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -26.31   26.31     1      1.00e+01 1.00e-02 9.95e+00
  ... (remaining 2700 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 365
       0.031 -    0.062: 175
       0.062 -    0.093: 71
       0.093 -    0.124: 33
       0.124 -    0.155: 15
  Chirality restraints: 659
  Sorted by residual:
  chirality pdb=" CA  ILE L  48 "
            pdb=" N   ILE L  48 "
            pdb=" C   ILE L  48 "
            pdb=" CB  ILE L  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.99e-01
  chirality pdb=" CA  ILE H  37 "
            pdb=" N   ILE H  37 "
            pdb=" C   ILE H  37 "
            pdb=" CB  ILE H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" CA  ILE B 402 "
            pdb=" N   ILE B 402 "
            pdb=" C   ILE B 402 "
            pdb=" CB  ILE B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.73e-01
  ... (remaining 656 not shown)

  Planarity restraints: 820
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 457 "    0.479 9.50e-02 1.11e+02   2.16e-01 3.63e+01
        pdb=" NE  ARG B 457 "   -0.046 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 457 "    0.044 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 457 "   -0.019 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 457 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 408 "    0.369 9.50e-02 1.11e+02   1.67e-01 2.15e+01
        pdb=" NE  ARG A 408 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 408 "    0.033 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 408 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 408 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 355 "    0.191 9.50e-02 1.11e+02   8.65e-02 6.00e+00
        pdb=" NE  ARG B 355 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 355 "    0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 355 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 355 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 817 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1466
        2.83 -     3.35: 3712
        3.35 -     3.87: 6515
        3.87 -     4.38: 7635
        4.38 -     4.90: 13939
  Nonbonded interactions: 33267
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 355 "
            pdb=" OD1 ASP B 398 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" NH1 ARG A 357 "
            pdb=" O   ILE A 358 "
     model   vdw
     2.315 3.120
  nonbonded pdb=" N   LYS A 462 "
            pdb=" OE2 GLU A 465 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" OE1 GLU A 406 "
            pdb=" NE2 GLN A 409 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" OG  SER A 349 "
            pdb=" O   LEU A 452 "
     model   vdw
     2.359 3.040
  ... (remaining 33262 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 338 through 358 or resid 366 through 380 or resid 394 thro \ 
ugh 515))
  selection = (chain 'B' and (resid 338 through 358 or resid 366 through 458 or (resid 459 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 460 through 515)) \ 

}

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:             6.830
  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:             0.020
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     5.940
  Find NCS groups from input model:        0.070
  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:6.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4671  Z= 0.116
  Angle     :  0.676   7.352   6353  Z= 0.367
  Chirality :  0.048   0.155    659
  Planarity :  0.012   0.216    820
  Dihedral  : 12.207  84.510   1641
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.40 (0.33), residues: 555
  helix: -3.86 (0.58), residues: 32
  sheet:  0.20 (0.41), residues: 170
  loop : -1.27 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.049   0.004   ARG B 457 
 TYR   0.021   0.003   TYR L  49 
 PHE   0.016   0.002   PHE A 377 
 TRP   0.017   0.002   TRP A 353 
 HIS   0.003   0.001   HIS H  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4665)
  covalent geometry    : angle       0.67382 ( 6341)
  SS BOND              : bond        0.00637 (    6)
  SS BOND              : angle       1.52209 (   12)
  hydrogen bonds       : bond        0.26923 (  128)
  hydrogen bonds       : angle       9.31830 (  315)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.142 
Fit side-chains
REVERT: B  444 LYS cc_start: 0.6749 (ttmm) cc_final: 0.6480 (tppt)
REVERT: L   45 LYS cc_start: 0.8337 (ptmm) cc_final: 0.7931 (pttt)
  outliers start: 0
  outliers final: 1
  residues processed: 130
  average time/residue: 0.4532
  time to fit residues: 61.2830
Evaluate side-chains
  81 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   78 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.135226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.112692 restraints weight = 6335.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.95
r_work: 0.3264 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   4671  Z= 0.164
  Angle     :  0.678  12.806   6353  Z= 0.354
  Chirality :  0.049   0.171    659
  Planarity :  0.005   0.033    820
  Dihedral  :  4.699  28.553    637
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.22 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.97 (0.33), residues: 555
  helix: -3.51 (0.67), residues: 33
  sheet:  0.81 (0.42), residues: 164
  loop : -1.12 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 466 
 TYR   0.014   0.002   TYR A 369 
 PHE   0.014   0.002   PHE B 347 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.002   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 4665)
  covalent geometry    : angle       0.66749 ( 6341)
  SS BOND              : bond        0.01118 (    6)
  SS BOND              : angle       2.75478 (   12)
  hydrogen bonds       : bond        0.03980 (  128)
  hydrogen bonds       : angle       6.47211 (  315)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  427 ASP cc_start: 0.8712 (m-30) cc_final: 0.8485 (t0)
REVERT: A  466 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7480 (ttm110)
REVERT: B  444 LYS cc_start: 0.7196 (ttmm) cc_final: 0.6871 (ttmt)
REVERT: B  498 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7972 (mt0)
REVERT: B  512 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8785 (t)
REVERT: L    4 MET cc_start: 0.7468 (mpp) cc_final: 0.7252 (mtm)
REVERT: L   11 LEU cc_start: 0.7518 (tp) cc_final: 0.7258 (mt)
REVERT: L   45 LYS cc_start: 0.8824 (ptmm) cc_final: 0.8514 (pttt)
  outliers start: 12
  outliers final: 3
  residues processed: 104
  average time/residue: 0.5553
  time to fit residues: 59.7573
Evaluate side-chains
  86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0670
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0570
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.4036

-------------------------------------------------------------------------------
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 = 0.3709 r_free = 0.3709 target = 0.135208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.112950 restraints weight = 6399.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.97
r_work: 0.3271 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   4671  Z= 0.115
  Angle     :  0.564  11.809   6353  Z= 0.296
  Chirality :  0.045   0.164    659
  Planarity :  0.004   0.031    820
  Dihedral  :  4.076  18.142    635
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 15.27 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.74 (0.33), residues: 555
  helix: -3.49 (0.74), residues: 28
  sheet:  0.98 (0.41), residues: 167
  loop : -1.01 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 346 
 TYR   0.009   0.001   TYR A 369 
 PHE   0.011   0.001   PHE A 400 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 4665)
  covalent geometry    : angle       0.55724 ( 6341)
  SS BOND              : bond        0.00926 (    6)
  SS BOND              : angle       2.07143 (   12)
  hydrogen bonds       : bond        0.03629 (  128)
  hydrogen bonds       : angle       6.12100 (  315)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  427 ASP cc_start: 0.8746 (m-30) cc_final: 0.8470 (t0)
REVERT: A  466 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7526 (ttm110)
REVERT: A  506 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8536 (mt0)
REVERT: B  444 LYS cc_start: 0.7207 (ttmm) cc_final: 0.6890 (ttmt)
REVERT: B  498 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7925 (mt0)
REVERT: H    5 GLN cc_start: 0.7922 (mp10) cc_final: 0.7640 (mp10)
REVERT: L    4 MET cc_start: 0.7445 (mpp) cc_final: 0.7173 (mtm)
REVERT: L   45 LYS cc_start: 0.8799 (ptmm) cc_final: 0.8553 (pttt)
  outliers start: 13
  outliers final: 8
  residues processed: 91
  average time/residue: 0.6120
  time to fit residues: 57.5118
Evaluate side-chains
  88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
B 414 GLN
H   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.131012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.107829 restraints weight = 6761.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.13
r_work: 0.3216 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.4049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   4671  Z= 0.185
  Angle     :  0.683  14.908   6353  Z= 0.360
  Chirality :  0.048   0.218    659
  Planarity :  0.005   0.042    820
  Dihedral  :  4.711  18.606    635
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.27 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.84 (0.33), residues: 555
  helix: -3.76 (0.54), residues: 32
  sheet:  0.92 (0.41), residues: 180
  loop : -1.11 (0.29), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  24 
 TYR   0.018   0.002   TYR A 369 
 PHE   0.017   0.002   PHE B 338 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 4665)
  covalent geometry    : angle       0.67181 ( 6341)
  SS BOND              : bond        0.01262 (    6)
  SS BOND              : angle       2.93894 (   12)
  hydrogen bonds       : bond        0.04751 (  128)
  hydrogen bonds       : angle       6.47265 (  315)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  427 ASP cc_start: 0.8825 (m-30) cc_final: 0.8415 (t0)
REVERT: A  466 ARG cc_start: 0.7756 (ttp-110) cc_final: 0.7523 (ttm110)
REVERT: B  444 LYS cc_start: 0.7125 (ttmm) cc_final: 0.6800 (ttmt)
REVERT: B  498 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7863 (mt0)
REVERT: B  512 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8867 (t)
REVERT: H    5 GLN cc_start: 0.7926 (mp10) cc_final: 0.7629 (mp10)
REVERT: H   16 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7602 (mt-10)
REVERT: L    4 MET cc_start: 0.7833 (mpp) cc_final: 0.7607 (mtm)
REVERT: L   42 LYS cc_start: 0.8325 (mmtp) cc_final: 0.7972 (mtmt)
  outliers start: 16
  outliers final: 9
  residues processed: 92
  average time/residue: 0.6278
  time to fit residues: 59.7044
Evaluate side-chains
  91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.9762

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.130212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.107157 restraints weight = 6731.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.11
r_work: 0.3206 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   4671  Z= 0.181
  Angle     :  0.668  13.936   6353  Z= 0.353
  Chirality :  0.048   0.193    659
  Planarity :  0.005   0.044    820
  Dihedral  :  4.793  19.368    635
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 16.29 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.90 (0.33), residues: 555
  helix: -3.84 (0.52), residues: 32
  sheet:  0.99 (0.42), residues: 179
  loop : -1.21 (0.28), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  24 
 TYR   0.015   0.002   TYR A 489 
 PHE   0.016   0.002   PHE B 377 
 TRP   0.012   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 4665)
  covalent geometry    : angle       0.65764 ( 6341)
  SS BOND              : bond        0.01248 (    6)
  SS BOND              : angle       2.81864 (   12)
  hydrogen bonds       : bond        0.04587 (  128)
  hydrogen bonds       : angle       6.51313 (  315)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A  408 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8236 (ttm-80)
REVERT: A  427 ASP cc_start: 0.8826 (m-30) cc_final: 0.8382 (t0)
REVERT: A  465 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7486 (pt0)
REVERT: A  466 ARG cc_start: 0.7727 (ttp-110) cc_final: 0.7403 (ttm110)
REVERT: B  444 LYS cc_start: 0.7165 (ttmm) cc_final: 0.6846 (ttmt)
REVERT: B  498 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7852 (mt0)
REVERT: B  512 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8772 (t)
REVERT: H    5 GLN cc_start: 0.7959 (mp10) cc_final: 0.7673 (mp10)
REVERT: H   16 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7596 (mt-10)
REVERT: H   63 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6987 (mt)
REVERT: L   42 LYS cc_start: 0.8348 (mmtp) cc_final: 0.7972 (mtmt)
  outliers start: 20
  outliers final: 11
  residues processed: 94
  average time/residue: 0.6601
  time to fit residues: 63.9770
Evaluate side-chains
  97 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   63 LEU
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain L residue  100 GLN
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.129953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.107894 restraints weight = 6491.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.95
r_work: 0.3206 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.4401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   4671  Z= 0.142
  Angle     :  0.611  13.039   6353  Z= 0.324
  Chirality :  0.046   0.192    659
  Planarity :  0.005   0.044    820
  Dihedral  :  4.558  20.122    635
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 17.92 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.85 (0.33), residues: 555
  helix: -4.00 (0.60), residues: 27
  sheet:  1.15 (0.42), residues: 175
  loop : -1.26 (0.28), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  24 
 TYR   0.012   0.001   TYR A 369 
 PHE   0.012   0.001   PHE B 377 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4665)
  covalent geometry    : angle       0.60265 ( 6341)
  SS BOND              : bond        0.01084 (    6)
  SS BOND              : angle       2.41263 (   12)
  hydrogen bonds       : bond        0.04000 (  128)
  hydrogen bonds       : angle       6.34690 (  315)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  408 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8242 (ttm-80)
REVERT: A  427 ASP cc_start: 0.8794 (m-30) cc_final: 0.8388 (t0)
REVERT: A  466 ARG cc_start: 0.7749 (ttp-110) cc_final: 0.7454 (ttm110)
REVERT: B  444 LYS cc_start: 0.7246 (ttmm) cc_final: 0.6957 (ttmt)
REVERT: B  498 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7887 (mt0)
REVERT: B  512 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8783 (t)
REVERT: H   16 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7587 (mt-10)
REVERT: H   63 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6974 (mt)
REVERT: L   42 LYS cc_start: 0.8356 (mmtp) cc_final: 0.7981 (mtmt)
  outliers start: 18
  outliers final: 10
  residues processed: 91
  average time/residue: 0.6025
  time to fit residues: 56.7299
Evaluate side-chains
  92 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   63 LEU
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0770
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 21 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.130907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.109098 restraints weight = 6511.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.92
r_work: 0.3219 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.4455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   4671  Z= 0.128
  Angle     :  0.588  11.963   6353  Z= 0.311
  Chirality :  0.045   0.169    659
  Planarity :  0.005   0.041    820
  Dihedral  :  4.409  20.994    635
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 19.14 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.78 (0.33), residues: 555
  helix: -3.95 (0.61), residues: 27
  sheet:  1.18 (0.41), residues: 174
  loop : -1.19 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  24 
 TYR   0.015   0.001   TYR A 489 
 PHE   0.011   0.001   PHE B 377 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4665)
  covalent geometry    : angle       0.58083 ( 6341)
  SS BOND              : bond        0.00999 (    6)
  SS BOND              : angle       2.16745 (   12)
  hydrogen bonds       : bond        0.03731 (  128)
  hydrogen bonds       : angle       6.22392 (  315)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A  408 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8270 (ttm-80)
REVERT: A  424 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8857 (tmtm)
REVERT: A  427 ASP cc_start: 0.8752 (m-30) cc_final: 0.8375 (t0)
REVERT: A  465 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7488 (pt0)
REVERT: A  466 ARG cc_start: 0.7695 (ttp-110) cc_final: 0.7475 (ttm110)
REVERT: B  444 LYS cc_start: 0.7274 (ttmm) cc_final: 0.6904 (tppt)
REVERT: B  498 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7941 (mt0)
REVERT: L   42 LYS cc_start: 0.8356 (mmtp) cc_final: 0.8053 (mtmt)
  outliers start: 18
  outliers final: 9
  residues processed: 91
  average time/residue: 0.6157
  time to fit residues: 58.0111
Evaluate side-chains
  91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 34 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0970
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.130332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.108528 restraints weight = 6531.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.93
r_work: 0.3210 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.4556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   4671  Z= 0.136
  Angle     :  0.603  11.901   6353  Z= 0.317
  Chirality :  0.045   0.171    659
  Planarity :  0.005   0.040    820
  Dihedral  :  4.467  21.270    635
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 19.96 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.74 (0.33), residues: 555
  helix: -3.96 (0.60), residues: 27
  sheet:  1.24 (0.41), residues: 174
  loop : -1.19 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 346 
 TYR   0.017   0.001   TYR A 489 
 PHE   0.011   0.001   PHE B 377 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4665)
  covalent geometry    : angle       0.59530 ( 6341)
  SS BOND              : bond        0.01036 (    6)
  SS BOND              : angle       2.25948 (   12)
  hydrogen bonds       : bond        0.03905 (  128)
  hydrogen bonds       : angle       6.26313 (  315)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  408 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8250 (ttm-80)
REVERT: A  424 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8852 (tmtm)
REVERT: A  427 ASP cc_start: 0.8750 (m-30) cc_final: 0.8367 (t0)
REVERT: A  465 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7492 (pt0)
REVERT: A  466 ARG cc_start: 0.7718 (ttp-110) cc_final: 0.7499 (ttm110)
REVERT: B  444 LYS cc_start: 0.7264 (ttmm) cc_final: 0.6885 (tppt)
REVERT: B  498 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7942 (mt0)
REVERT: B  512 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8762 (t)
REVERT: L   42 LYS cc_start: 0.8369 (mmtp) cc_final: 0.8087 (mtmt)
  outliers start: 17
  outliers final: 11
  residues processed: 88
  average time/residue: 0.6312
  time to fit residues: 57.4549
Evaluate side-chains
  92 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue   81 LYS
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 24 optimal weight:    0.1980
   chunk 46 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.132098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.110489 restraints weight = 6463.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.91
r_work: 0.3242 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.4573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   4671  Z= 0.110
  Angle     :  0.557  10.536   6353  Z= 0.293
  Chirality :  0.044   0.162    659
  Planarity :  0.004   0.034    820
  Dihedral  :  4.223  21.121    635
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.37 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.69 (0.33), residues: 555
  helix: -3.68 (0.56), residues: 33
  sheet:  1.25 (0.42), residues: 170
  loop : -1.06 (0.28), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 346 
 TYR   0.010   0.001   TYR A 369 
 PHE   0.009   0.001   PHE B 377 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4665)
  covalent geometry    : angle       0.55160 ( 6341)
  SS BOND              : bond        0.00866 (    6)
  SS BOND              : angle       1.85072 (   12)
  hydrogen bonds       : bond        0.03349 (  128)
  hydrogen bonds       : angle       6.13785 (  315)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  424 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8828 (tmtm)
REVERT: A  427 ASP cc_start: 0.8729 (m-30) cc_final: 0.8399 (t0)
REVERT: A  466 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7453 (ttm110)
REVERT: A  503 VAL cc_start: 0.8499 (p) cc_final: 0.8270 (p)
REVERT: B  444 LYS cc_start: 0.7257 (ttmm) cc_final: 0.6889 (tppt)
REVERT: B  498 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7934 (mt0)
REVERT: L   42 LYS cc_start: 0.8319 (mmtp) cc_final: 0.8026 (mtmt)
  outliers start: 16
  outliers final: 9
  residues processed: 89
  average time/residue: 0.5732
  time to fit residues: 52.8519
Evaluate side-chains
  87 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain L residue  103 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0870
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0670
   chunk 32 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   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 450 ASN
H   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.133971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.111261 restraints weight = 6846.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.17
r_work: 0.3267 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   4671  Z= 0.115
  Angle     :  0.560  10.517   6353  Z= 0.295
  Chirality :  0.044   0.163    659
  Planarity :  0.004   0.032    820
  Dihedral  :  4.210  21.426    635
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.18 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.65 (0.33), residues: 555
  helix: -3.63 (0.58), residues: 33
  sheet:  1.25 (0.42), residues: 170
  loop : -1.03 (0.28), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 346 
 TYR   0.011   0.001   TYR A 369 
 PHE   0.009   0.001   PHE B 377 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.000   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4665)
  covalent geometry    : angle       0.55353 ( 6341)
  SS BOND              : bond        0.00973 (    6)
  SS BOND              : angle       1.98426 (   12)
  hydrogen bonds       : bond        0.03510 (  128)
  hydrogen bonds       : angle       6.16144 (  315)

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

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

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1110 Ramachandran restraints generated.
    555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.7976 (mp0) cc_final: 0.7628 (mp0)
REVERT: A  424 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8853 (tmtm)
REVERT: A  427 ASP cc_start: 0.8761 (m-30) cc_final: 0.8396 (t0)
REVERT: A  466 ARG cc_start: 0.7647 (ttp-110) cc_final: 0.7432 (ttm110)
REVERT: A  503 VAL cc_start: 0.8502 (p) cc_final: 0.8270 (p)
REVERT: B  444 LYS cc_start: 0.7219 (ttmm) cc_final: 0.6754 (tppt)
REVERT: B  498 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7934 (mt0)
REVERT: H   81 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8582 (mppt)
REVERT: L   42 LYS cc_start: 0.8366 (mmtp) cc_final: 0.7921 (mtmt)
  outliers start: 13
  outliers final: 8
  residues processed: 84
  average time/residue: 0.6172
  time to fit residues: 53.6613
Evaluate side-chains
  87 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain H residue   65 ASN
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue   81 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.0170
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.130352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.108774 restraints weight = 6464.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.91
r_work: 0.3218 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   4671  Z= 0.133
  Angle     :  0.596  11.105   6353  Z= 0.313
  Chirality :  0.045   0.160    659
  Planarity :  0.004   0.031    820
  Dihedral  :  4.357  21.251    635
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 20.37 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.70 (0.34), residues: 555
  helix: -3.67 (0.57), residues: 33
  sheet:  1.03 (0.41), residues: 181
  loop : -1.01 (0.29), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 346 
 TYR   0.014   0.001   TYR A 489 
 PHE   0.010   0.001   PHE B 377 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4665)
  covalent geometry    : angle       0.58913 ( 6341)
  SS BOND              : bond        0.01064 (    6)
  SS BOND              : angle       2.19342 (   12)
  hydrogen bonds       : bond        0.03861 (  128)
  hydrogen bonds       : angle       6.21011 (  315)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2037.26 seconds
wall clock time: 35 minutes 25.74 seconds (2125.74 seconds total)