Starting phenix.real_space_refine
on Thu Mar  6 02:46:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tm1_41374/03_2025/8tm1_41374.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tm1_41374/03_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_41374/03_2025/8tm1_41374.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tm1_41374/03_2025/8tm1_41374.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tm1_41374/03_2025/8tm1_41374.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tm1_41374/03_2025/8tm1_41374.cif"
  }
  resolution = 2.79
  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=  -0.008 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.50, per 1000 atoms: 0.99
  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: 0.90
  Conformation dependent library (CDL) restraints added in 487.7 milliseconds
  

  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: 0.65
  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: 1.16

  Time building geometry restraints manager: 1.12 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:             14.900
  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:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.360
  Find NCS groups from input model:        0.140
  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:18.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.860
-------------------------------------------------------------------------------
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   4665  Z= 0.163
  Angle     :  0.674   7.352   6341  Z= 0.366
  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 (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: -1.40 (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
 TRP   0.017   0.002   TRP A 353 
 HIS   0.003   0.001   HIS H  77 
 PHE   0.016   0.002   PHE A 377 
 TYR   0.021   0.003   TYR L  49 
 ARG   0.049   0.004   ARG B 457 

*********************** 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  : 0.479 
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: 1.0271
  time to fit residues: 139.5946
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  : 0.518 
-------------------------------------------------------------------------------
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 45 optimal weight:    0.0170
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 13 optimal weight:    0.2980
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    0.2980
   chunk 42 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.3218

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.139806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.117564 restraints weight = 6310.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.94
r_work: 0.3344 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   4665  Z= 0.174
  Angle     :  0.588  11.876   6341  Z= 0.306
  Chirality :  0.046   0.164    659
  Planarity :  0.004   0.035    820
  Dihedral  :  4.220  31.153    637
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.42 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.94 (0.33), residues: 555
  helix: -3.51 (0.64), residues: 33
  sheet:  0.66 (0.41), residues: 170
  loop : -1.02 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.000   HIS H 101 
 PHE   0.011   0.001   PHE A 377 
 TYR   0.011   0.001   TYR A 369 
 ARG   0.010   0.001   ARG A 346 

*********************** 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
  101 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  442 ASP cc_start: 0.7265 (m-30) cc_final: 0.6815 (m-30)
REVERT: A  466 ARG cc_start: 0.7602 (ttp-110) cc_final: 0.7170 (ttm110)
REVERT: B  444 LYS cc_start: 0.7191 (ttmm) cc_final: 0.6805 (tppt)
REVERT: B  465 GLU cc_start: 0.8306 (tt0) cc_final: 0.8098 (tt0)
REVERT: L    4 MET cc_start: 0.7335 (mpp) cc_final: 0.7124 (mtm)
REVERT: L   45 LYS cc_start: 0.8607 (ptmm) cc_final: 0.8238 (pttt)
  outliers start: 8
  outliers final: 3
  residues processed: 100
  average time/residue: 1.2448
  time to fit residues: 129.1911
Evaluate side-chains
  84 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain H residue   78 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0470
   chunk 15 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0050
   chunk 50 optimal weight:    0.0870
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.2670

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

Flipped N/Q/H residues before XYZ refinement:
A 440 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.138894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.116416 restraints weight = 6427.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.97
r_work: 0.3325 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   4665  Z= 0.150
  Angle     :  0.521   9.896   6341  Z= 0.273
  Chirality :  0.044   0.155    659
  Planarity :  0.004   0.032    820
  Dihedral  :  3.962  31.232    637
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.46 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.62 (0.33), residues: 555
  helix: -3.30 (0.74), residues: 28
  sheet:  0.92 (0.41), residues: 167
  loop : -0.86 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.001   0.001   HIS H  77 
 PHE   0.010   0.001   PHE A 400 
 TYR   0.010   0.001   TYR A 369 
 ARG   0.004   0.001   ARG A 457 

*********************** 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
  94 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A  408 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8392 (ttm-80)
REVERT: A  442 ASP cc_start: 0.7332 (m-30) cc_final: 0.6884 (m-30)
REVERT: A  466 ARG cc_start: 0.7718 (ttp-110) cc_final: 0.7321 (ttm110)
REVERT: B  444 LYS cc_start: 0.7166 (ttmm) cc_final: 0.6868 (ttmt)
REVERT: B  498 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7906 (mt0)
REVERT: L    4 MET cc_start: 0.7402 (mpp) cc_final: 0.7051 (mtm)
REVERT: L   42 LYS cc_start: 0.7935 (mmtp) cc_final: 0.7694 (mtmt)
REVERT: L   45 LYS cc_start: 0.8669 (ptmm) cc_final: 0.8337 (pttt)
  outliers start: 10
  outliers final: 4
  residues processed: 93
  average time/residue: 1.2067
  time to fit residues: 116.3288
Evaluate side-chains
  87 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 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  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:    0.0070
   chunk 36 optimal weight:    0.0970
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    0.3980
   chunk 16 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
B 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.136167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.113439 restraints weight = 6510.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.01
r_work: 0.3285 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   4665  Z= 0.166
  Angle     :  0.529  11.284   6341  Z= 0.278
  Chirality :  0.044   0.162    659
  Planarity :  0.004   0.030    820
  Dihedral  :  3.861  18.235    635
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 14.66 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.58 (0.33), residues: 555
  helix: -3.19 (0.78), residues: 28
  sheet:  0.87 (0.41), residues: 173
  loop : -0.82 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H  77 
 PHE   0.012   0.001   PHE B 377 
 TYR   0.014   0.001   TYR A 489 
 ARG   0.004   0.001   ARG L  24 

*********************** 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
  104 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.8617 (ttp-170) cc_final: 0.8264 (ttp-170)
REVERT: A  408 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8346 (ttm-80)
REVERT: A  466 ARG cc_start: 0.7757 (ttp-110) cc_final: 0.7438 (ttm110)
REVERT: B  444 LYS cc_start: 0.7179 (ttmm) cc_final: 0.6846 (ttmt)
REVERT: B  498 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7912 (mt0)
REVERT: H    5 GLN cc_start: 0.7907 (mp10) cc_final: 0.7643 (mp10)
REVERT: L    4 MET cc_start: 0.7370 (mpp) cc_final: 0.7090 (mtm)
REVERT: L   42 LYS cc_start: 0.8081 (mmtp) cc_final: 0.7792 (mtmt)
REVERT: L   45 LYS cc_start: 0.8812 (ptmm) cc_final: 0.8531 (pttt)
  outliers start: 17
  outliers final: 8
  residues processed: 98
  average time/residue: 1.2649
  time to fit residues: 128.3684
Evaluate side-chains
  93 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
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  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  474 GLN
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0670
   chunk 49 optimal weight:    3.9990
   chunk 36 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8720

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

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

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 = 0.131009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.108641 restraints weight = 6496.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.94
r_work: 0.3211 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.3971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   4665  Z= 0.273
  Angle     :  0.650  13.796   6341  Z= 0.344
  Chirality :  0.048   0.217    659
  Planarity :  0.005   0.054    820
  Dihedral  :  4.544  18.781    635
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 14.87 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.63 (0.33), residues: 555
  helix: -3.35 (0.67), residues: 33
  sheet:  1.39 (0.43), residues: 164
  loop : -1.07 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H 101 
 PHE   0.018   0.002   PHE B 338 
 TYR   0.017   0.002   TYR A 369 
 ARG   0.013   0.001   ARG L  24 

*********************** 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: 19
    poor density    : 83
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8690 (ttp-170) cc_final: 0.8394 (ttp-170)
REVERT: A  408 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8389 (ttm-80)
REVERT: A  506 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8440 (mt0)
REVERT: B  444 LYS cc_start: 0.7253 (ttmm) cc_final: 0.6964 (ttmt)
REVERT: B  498 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7917 (mt0)
REVERT: B  512 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8791 (t)
REVERT: H    5 GLN cc_start: 0.8046 (mp10) cc_final: 0.7789 (mp10)
REVERT: L    4 MET cc_start: 0.7600 (mpp) cc_final: 0.7366 (mtm)
REVERT: L   42 LYS cc_start: 0.8358 (mmtp) cc_final: 0.8065 (mtmt)
  outliers start: 19
  outliers final: 10
  residues processed: 96
  average time/residue: 1.3056
  time to fit residues: 129.5957
Evaluate side-chains
  94 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
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  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  378 LYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 9 optimal weight:    0.2980
   chunk 6 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 36 optimal weight:    0.2980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.132111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.110064 restraints weight = 6396.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.92
r_work: 0.3236 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.4152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   4665  Z= 0.199
  Angle     :  0.577  12.573   6341  Z= 0.306
  Chirality :  0.045   0.179    659
  Planarity :  0.005   0.054    820
  Dihedral  :  4.294  19.777    635
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.48 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.65 (0.33), residues: 555
  helix: -3.43 (0.76), residues: 28
  sheet:  1.14 (0.42), residues: 170
  loop : -1.02 (0.28), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H 101 
 PHE   0.012   0.001   PHE B 377 
 TYR   0.015   0.001   TYR A 489 
 ARG   0.012   0.001   ARG L  24 

*********************** 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
  102 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.7969 (mp0) cc_final: 0.7581 (mp0)
REVERT: A  403 ARG cc_start: 0.8667 (ttp-170) cc_final: 0.8318 (ttp-170)
REVERT: A  408 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8312 (ttm-80)
REVERT: A  506 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8356 (mt0)
REVERT: B  444 LYS cc_start: 0.7261 (ttmm) cc_final: 0.6986 (ttmt)
REVERT: B  498 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7917 (mt0)
REVERT: H   63 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6856 (mt)
REVERT: L    4 MET cc_start: 0.7591 (mpp) cc_final: 0.7351 (mtm)
REVERT: L   42 LYS cc_start: 0.8355 (mmtp) cc_final: 0.8038 (mtmt)
  outliers start: 17
  outliers final: 10
  residues processed: 97
  average time/residue: 1.2611
  time to fit residues: 126.7613
Evaluate side-chains
  96 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
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  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
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 L residue  103 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 46 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.108327 restraints weight = 6338.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.94
r_work: 0.3206 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.4318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   4665  Z= 0.232
  Angle     :  0.612  12.621   6341  Z= 0.325
  Chirality :  0.046   0.181    659
  Planarity :  0.005   0.057    820
  Dihedral  :  4.475  20.180    635
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.11 %
    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 (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: -0.67 (0.33), residues: 555
  helix: -3.59 (0.71), residues: 28
  sheet:  1.23 (0.43), residues: 167
  loop : -1.06 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H 101 
 PHE   0.014   0.002   PHE B 338 
 TYR   0.014   0.001   TYR A 369 
 ARG   0.014   0.001   ARG L  24 

*********************** 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
  99 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.532 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.7959 (mp0) cc_final: 0.7573 (mp0)
REVERT: A  408 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8290 (ttm-80)
REVERT: A  506 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8352 (mt0)
REVERT: B  378 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7777 (ttpt)
REVERT: B  444 LYS cc_start: 0.7262 (ttmm) cc_final: 0.6923 (tppt)
REVERT: B  498 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7911 (mt0)
REVERT: B  512 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8740 (t)
REVERT: H   81 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8549 (mppt)
REVERT: L   42 LYS cc_start: 0.8336 (mmtp) cc_final: 0.8015 (mtmt)
  outliers start: 16
  outliers final: 8
  residues processed: 94
  average time/residue: 1.2063
  time to fit residues: 117.6544
Evaluate side-chains
  96 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
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  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  378 LYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0000
   chunk 0 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0980
   chunk 12 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN
H  77 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.132204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.110160 restraints weight = 6453.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.94
r_work: 0.3239 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.4381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   4665  Z= 0.183
  Angle     :  0.557  11.194   6341  Z= 0.296
  Chirality :  0.044   0.165    659
  Planarity :  0.004   0.038    820
  Dihedral  :  4.261  20.700    635
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.31 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.62 (0.33), residues: 555
  helix: -3.45 (0.63), residues: 34
  sheet:  1.14 (0.42), residues: 170
  loop : -0.93 (0.28), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H 101 
 PHE   0.011   0.001   PHE B 377 
 TYR   0.017   0.001   TYR A 489 
 ARG   0.008   0.001   ARG L  24 

*********************** 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
  102 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.8017 (mp0) cc_final: 0.7611 (mp0)
REVERT: A  403 ARG cc_start: 0.8675 (ttp-170) cc_final: 0.8332 (ttp-170)
REVERT: A  408 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8285 (ttm-80)
REVERT: A  506 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8347 (mt0)
REVERT: B  378 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7724 (ttpt)
REVERT: B  444 LYS cc_start: 0.7237 (ttmm) cc_final: 0.6869 (tppt)
REVERT: B  498 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7931 (mt0)
REVERT: H   81 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8542 (mppt)
REVERT: L   42 LYS cc_start: 0.8303 (mmtp) cc_final: 0.8004 (mtmt)
  outliers start: 16
  outliers final: 10
  residues processed: 96
  average time/residue: 1.1636
  time to fit residues: 115.9512
Evaluate side-chains
  100 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
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  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  378 LYS
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  103 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 10 optimal weight:    0.3980
   chunk 36 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 38 optimal weight:    0.4980
   chunk 9 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3665 r_free = 0.3665 target = 0.131770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.109710 restraints weight = 6456.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.97
r_work: 0.3241 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.4434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   4665  Z= 0.184
  Angle     :  0.559  10.924   6341  Z= 0.296
  Chirality :  0.044   0.165    659
  Planarity :  0.004   0.038    820
  Dihedral  :  4.214  21.097    635
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.33 %
    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 (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: -0.57 (0.34), residues: 555
  helix: -3.42 (0.64), residues: 34
  sheet:  1.18 (0.42), residues: 170
  loop : -0.89 (0.29), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.000   HIS H 101 
 PHE   0.011   0.001   PHE B 377 
 TYR   0.016   0.001   TYR A 489 
 ARG   0.007   0.001   ARG A 346 

*********************** 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
  100 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.513 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.8011 (mp0) cc_final: 0.7554 (mp0)
REVERT: A  403 ARG cc_start: 0.8684 (ttp-170) cc_final: 0.8472 (ttp-170)
REVERT: A  408 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8237 (ttm-80)
REVERT: A  506 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8299 (mt0)
REVERT: B  378 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7671 (ttpt)
REVERT: B  444 LYS cc_start: 0.7211 (ttmm) cc_final: 0.6837 (tppt)
REVERT: B  498 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7910 (mt0)
REVERT: H   81 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8523 (mppt)
REVERT: L   42 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7921 (mtmt)
  outliers start: 16
  outliers final: 10
  residues processed: 94
  average time/residue: 1.2326
  time to fit residues: 120.3228
Evaluate side-chains
  97 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
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  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  378 LYS
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  103 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0670
   chunk 20 optimal weight:    0.8980
   chunk 36 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0270
   chunk 44 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0570
   chunk 4 optimal weight:    0.0060
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.0710

-------------------------------------------------------------------------------
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 = 0.3741 r_free = 0.3741 target = 0.137609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.116021 restraints weight = 6451.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.96
r_work: 0.3337 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.4513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   4665  Z= 0.127
  Angle     :  0.484   8.011   6341  Z= 0.256
  Chirality :  0.042   0.151    659
  Planarity :  0.004   0.038    820
  Dihedral  :  3.718  19.554    635
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 20.57 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.37 (0.34), residues: 555
  helix: -3.20 (0.68), residues: 34
  sheet:  1.19 (0.42), residues: 170
  loop : -0.69 (0.29), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 436 
 HIS   0.001   0.000   HIS H 101 
 PHE   0.013   0.001   PHE A 400 
 TYR   0.012   0.001   TYR A 489 
 ARG   0.008   0.001   ARG L  24 

********************** 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
  93 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A  340 GLU cc_start: 0.8043 (mp0) cc_final: 0.7584 (mp0)
REVERT: A  403 ARG cc_start: 0.8419 (ttp-170) cc_final: 0.8120 (ttp-170)
REVERT: A  506 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8117 (mt0)
REVERT: B  378 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7606 (ttpt)
REVERT: B  444 LYS cc_start: 0.7202 (ttmm) cc_final: 0.6808 (tppt)
REVERT: H    4 LEU cc_start: 0.8753 (mp) cc_final: 0.8375 (mt)
REVERT: H   81 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8553 (mppt)
REVERT: L   42 LYS cc_start: 0.8023 (mmtp) cc_final: 0.7674 (mtmt)
  outliers start: 8
  outliers final: 5
  residues processed: 90
  average time/residue: 1.2317
  time to fit residues: 115.1180
Evaluate side-chains
  91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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  465 GLU
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain B residue  378 LYS
Chi-restraints excluded: chain B residue  512 VAL
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 25 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.8580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.129999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.108101 restraints weight = 6398.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.95
r_work: 0.3217 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.4555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   4665  Z= 0.261
  Angle     :  0.620  11.557   6341  Z= 0.327
  Chirality :  0.046   0.171    659
  Planarity :  0.005   0.040    820
  Dihedral  :  4.340  20.726    635
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.96 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.47 (0.34), residues: 555
  helix: -3.41 (0.64), residues: 34
  sheet:  1.37 (0.43), residues: 167
  loop : -0.87 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H  40 
 PHE   0.017   0.002   PHE B 338 
 TYR   0.014   0.002   TYR A 369 
 ARG   0.008   0.001   ARG B 346 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4335.59 seconds
wall clock time: 75 minutes 1.88 seconds (4501.88 seconds total)