Starting phenix.real_space_refine
on Tue Feb 11 06:57:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tm1_41374/02_2025/8tm1_41374.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tm1_41374/02_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_41374/02_2025/8tm1_41374.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tm1_41374/02_2025/8tm1_41374.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tm1_41374/02_2025/8tm1_41374.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tm1_41374/02_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-5592/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: 4.68, per 1000 atoms: 1.03
  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: 1.03
  Conformation dependent library (CDL) restraints added in 565.8 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: 0.60
  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: 1.12

  Time building geometry restraints manager: 1.23 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:             5.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.360
  Find NCS groups from input model:        0.120
  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:12.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.760
-------------------------------------------------------------------------------
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  : 0.560 
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: 1.0371
  time to fit residues: 140.6395
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  : 0.535 
-------------------------------------------------------------------------------
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 = 0.139799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.117566 restraints weight = 6310.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.94
r_work: 0.3342 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
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  : 0.535 
Fit side-chains
REVERT: A  442 ASP cc_start: 0.7261 (m-30) cc_final: 0.6809 (m-30)
REVERT: A  466 ARG cc_start: 0.7597 (ttp-110) cc_final: 0.7165 (ttm110)
REVERT: B  444 LYS cc_start: 0.7196 (ttmm) cc_final: 0.6819 (tppt)
REVERT: B  465 GLU cc_start: 0.8301 (tt0) cc_final: 0.8090 (tt0)
REVERT: L    4 MET cc_start: 0.7333 (mpp) cc_final: 0.7128 (mtm)
REVERT: L   45 LYS cc_start: 0.8600 (ptmm) cc_final: 0.8231 (pttt)
  outliers start: 8
  outliers final: 3
  residues processed: 100
  average time/residue: 1.3238
  time to fit residues: 137.0202
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  : 0.520 
-------------------------------------------------------------------------------
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:    0.0050
   chunk 31 optimal weight:    0.4980
   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:    0.2306

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.139293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.116673 restraints weight = 6429.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.01
r_work: 0.3334 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3091

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= 0.145
  Angle     :  0.513   9.632   6341  Z= 0.268
  Chirality :  0.044   0.154    659
  Planarity :  0.004   0.032    820
  Dihedral  :  3.921  31.533    637
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.46 %
    Favored  : 83.30 %
  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: -0.61 (0.33), residues: 555
  helix: -3.32 (0.73), residues: 28
  sheet:  0.89 (0.41), residues: 168
  loop : -0.83 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.001   HIS H  77 
 PHE   0.011   0.001   PHE A 400 
 TYR   0.010   0.001   TYR A 369 
 ARG   0.005   0.000   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
  93 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.553 
Fit side-chains
REVERT: A  408 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8358 (ttm-80)
REVERT: A  442 ASP cc_start: 0.7303 (m-30) cc_final: 0.6884 (m-30)
REVERT: A  466 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.7248 (ttm110)
REVERT: B  444 LYS cc_start: 0.7181 (ttmm) cc_final: 0.6872 (ttmt)
REVERT: B  498 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7871 (mt0)
REVERT: L    4 MET cc_start: 0.7425 (mpp) cc_final: 0.7064 (mtm)
REVERT: L   42 LYS cc_start: 0.7878 (mmtp) cc_final: 0.7565 (mtmt)
REVERT: L   45 LYS cc_start: 0.8681 (ptmm) cc_final: 0.8307 (pttt)
  outliers start: 11
  outliers final: 4
  residues processed: 90
  average time/residue: 1.3097
  time to fit residues: 122.0549
Evaluate side-chains
  86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 36 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    0.3980
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    0.3980
   chunk 16 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.134360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.111615 restraints weight = 6470.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.00
r_work: 0.3267 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   4665  Z= 0.193
  Angle     :  0.564  12.151   6341  Z= 0.298
  Chirality :  0.045   0.168    659
  Planarity :  0.004   0.032    820
  Dihedral  :  4.072  18.306    635
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 14.26 %
    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 (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: -3.13 (0.71), residues: 33
  sheet:  1.00 (0.42), residues: 169
  loop : -0.92 (0.29), residues: 353

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   0.015   0.001   PHE B 377 
 TYR   0.014   0.001   TYR A 489 
 ARG   0.004   0.001   ARG B 355 

*********************** 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
  103 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.8656 (ttp-170) cc_final: 0.8265 (ttp-170)
REVERT: A  408 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8321 (ttm-80)
REVERT: A  466 ARG cc_start: 0.7674 (ttp-110) cc_final: 0.7441 (ttm110)
REVERT: A  506 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8353 (mt0)
REVERT: B  444 LYS cc_start: 0.7142 (ttmm) cc_final: 0.6801 (ttmt)
REVERT: B  498 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7884 (mt0)
REVERT: B  512 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8770 (t)
REVERT: H    5 GLN cc_start: 0.7935 (mp10) cc_final: 0.7654 (mp10)
REVERT: L    4 MET cc_start: 0.7453 (mpp) cc_final: 0.7160 (mtm)
REVERT: L   42 LYS cc_start: 0.8181 (mmtp) cc_final: 0.7824 (mtmt)
REVERT: L   45 LYS cc_start: 0.8900 (ptmm) cc_final: 0.8609 (pttt)
  outliers start: 18
  outliers final: 6
  residues processed: 97
  average time/residue: 1.3241
  time to fit residues: 132.9662
Evaluate side-chains
  92 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    0.0000
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0970
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0060
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.3800

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.135035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.112630 restraints weight = 6539.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.99
r_work: 0.3283 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.3846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.062   4665  Z= 0.162
  Angle     :  0.530  11.673   6341  Z= 0.280
  Chirality :  0.044   0.166    659
  Planarity :  0.004   0.046    820
  Dihedral  :  3.928  19.115    635
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.07 %
    Favored  : 81.67 %
  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: -3.33 (0.77), residues: 28
  sheet:  1.03 (0.41), residues: 171
  loop : -0.88 (0.28), residues: 356

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   0.011   0.001   PHE B 377 
 TYR   0.010   0.001   TYR A 369 
 ARG   0.008   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
  106 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.497 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.8577 (ttp-170) cc_final: 0.8083 (ttp-170)
REVERT: A  408 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8303 (ttm-80)
REVERT: A  506 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8228 (mt0)
REVERT: B  444 LYS cc_start: 0.7210 (ttmm) cc_final: 0.6755 (tppt)
REVERT: B  498 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7892 (mt0)
REVERT: H   81 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8413 (mppt)
REVERT: L    4 MET cc_start: 0.7497 (mpp) cc_final: 0.7160 (mtm)
REVERT: L   42 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7806 (mtmt)
REVERT: L   45 LYS cc_start: 0.8886 (ptmm) cc_final: 0.8631 (pttt)
  outliers start: 16
  outliers final: 10
  residues processed: 101
  average time/residue: 1.3059
  time to fit residues: 136.5993
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  : 0.540 
-------------------------------------------------------------------------------
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   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=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:    0.5980
   chunk 22 optimal weight:    0.4980
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.132187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.109873 restraints weight = 6423.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 1.97
r_work: 0.3238 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   4665  Z= 0.202
  Angle     :  0.574  12.333   6341  Z= 0.304
  Chirality :  0.045   0.174    659
  Planarity :  0.004   0.037    820
  Dihedral  :  4.181  19.649    635
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  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: -0.59 (0.33), residues: 555
  helix: -3.41 (0.76), residues: 28
  sheet:  1.14 (0.42), residues: 170
  loop : -0.96 (0.28), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H 101 
 PHE   0.013   0.001   PHE B 377 
 TYR   0.019   0.001   TYR A 489 
 ARG   0.009   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
  101 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.8678 (ttp-170) cc_final: 0.8241 (ttp-170)
REVERT: A  408 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8294 (ttm-80)
REVERT: A  506 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8297 (mt0)
REVERT: B  444 LYS cc_start: 0.7231 (ttmm) cc_final: 0.6934 (ttmt)
REVERT: B  498 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7880 (mt0)
REVERT: B  512 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8786 (t)
REVERT: H   63 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6956 (mt)
REVERT: L    3 GLN cc_start: 0.7701 (mm110) cc_final: 0.7397 (mm110)
REVERT: L    4 MET cc_start: 0.7619 (mpp) cc_final: 0.7353 (mtm)
REVERT: L   42 LYS cc_start: 0.8280 (mmtp) cc_final: 0.7920 (mtmt)
  outliers start: 16
  outliers final: 9
  residues processed: 96
  average time/residue: 1.2724
  time to fit residues: 126.6992
Evaluate side-chains
  95 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 46 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0770
   chunk 25 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 7 optimal weight:    0.3980
   chunk 28 optimal weight:    0.0370
   overall best weight:    0.3216

-------------------------------------------------------------------------------
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 = 0.3703 r_free = 0.3703 target = 0.134749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.112921 restraints weight = 6414.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.92
r_work: 0.3279 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059   4665  Z= 0.153
  Angle     :  0.521  10.494   6341  Z= 0.276
  Chirality :  0.043   0.158    659
  Planarity :  0.004   0.034    820
  Dihedral  :  3.943  19.828    635
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  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: -0.53 (0.33), residues: 555
  helix: -3.27 (0.67), residues: 34
  sheet:  1.12 (0.42), residues: 170
  loop : -0.83 (0.28), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.000   HIS H  77 
 PHE   0.009   0.001   PHE A 400 
 TYR   0.014   0.001   TYR A 489 
 ARG   0.008   0.001   ARG B 346 

*********************** 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
  94 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  408 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8308 (ttm-80)
REVERT: A  506 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8208 (mt0)
REVERT: B  378 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7645 (ttpt)
REVERT: B  444 LYS cc_start: 0.7209 (ttmm) cc_final: 0.6850 (tppt)
REVERT: B  498 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7937 (mt0)
REVERT: H   81 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8497 (mppt)
REVERT: L    3 GLN cc_start: 0.7725 (mm110) cc_final: 0.7450 (mm110)
REVERT: L    4 MET cc_start: 0.7539 (mpp) cc_final: 0.7310 (mtm)
REVERT: L   42 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7905 (mtmt)
  outliers start: 16
  outliers final: 8
  residues processed: 89
  average time/residue: 1.2792
  time to fit residues: 118.0918
Evaluate side-chains
  92 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
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  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:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B 414 GLN
H   5 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.128467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.105377 restraints weight = 6774.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.12
r_work: 0.3179 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
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      :  0.007   0.091   4665  Z= 0.426
  Angle     :  0.772  14.581   6341  Z= 0.408
  Chirality :  0.052   0.223    659
  Planarity :  0.006   0.050    820
  Dihedral  :  5.145  18.862    635
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 17.52 %
    Favored  : 79.02 %
  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: -0.76 (0.33), residues: 555
  helix: -3.52 (0.61), residues: 32
  sheet:  1.16 (0.41), residues: 176
  loop : -1.16 (0.28), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.003   0.001   HIS H  40 
 PHE   0.036   0.003   PHE B 338 
 TYR   0.022   0.003   TYR A 369 
 ARG   0.007   0.001   ARG H 100E

*********************** 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
  104 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A  408 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8359 (ttm-80)
REVERT: A  506 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8373 (mt0)
REVERT: B  444 LYS cc_start: 0.7215 (ttmm) cc_final: 0.6806 (tppt)
REVERT: B  498 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7849 (mt0)
REVERT: B  512 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8842 (t)
REVERT: L   42 LYS cc_start: 0.8367 (mmtp) cc_final: 0.7964 (mtmt)
  outliers start: 17
  outliers final: 8
  residues processed: 96
  average time/residue: 1.2632
  time to fit residues: 125.5835
Evaluate side-chains
  91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
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  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   65 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 40 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3642 r_free = 0.3642 target = 0.130078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.107950 restraints weight = 6469.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.96
r_work: 0.3210 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.4546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   4665  Z= 0.214
  Angle     :  0.597  12.024   6341  Z= 0.319
  Chirality :  0.046   0.171    659
  Planarity :  0.005   0.043    820
  Dihedral  :  4.596  20.410    635
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.74 %
    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: -0.72 (0.33), residues: 555
  helix: -3.80 (0.69), residues: 28
  sheet:  1.12 (0.41), residues: 176
  loop : -1.10 (0.28), residues: 351

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   0.013   0.001   PHE B 377 
 TYR   0.014   0.001   TYR A 489 
 ARG   0.008   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
  96 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A  408 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8204 (ttm-80)
REVERT: A  506 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8305 (mt0)
REVERT: B  444 LYS cc_start: 0.7238 (ttmm) cc_final: 0.6858 (tppt)
REVERT: B  498 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7891 (mt0)
REVERT: H    3 GLN cc_start: 0.8517 (mm110) cc_final: 0.8288 (mm-40)
REVERT: L   42 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7940 (mtmt)
  outliers start: 14
  outliers final: 7
  residues processed: 91
  average time/residue: 1.3335
  time to fit residues: 125.7171
Evaluate side-chains
  90 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9990
   chunk 36 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0060
   chunk 44 optimal weight:    0.4980
   chunk 13 optimal weight:    0.2980
   chunk 4 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0270
   overall best weight:    0.1854

-------------------------------------------------------------------------------
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 = 0.3709 r_free = 0.3709 target = 0.135104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.113590 restraints weight = 6434.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.91
r_work: 0.3296 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.4584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054   4665  Z= 0.141
  Angle     :  0.510   9.174   6341  Z= 0.270
  Chirality :  0.043   0.157    659
  Planarity :  0.004   0.035    820
  Dihedral  :  3.965  20.022    635
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 20.98 %
    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: -0.45 (0.34), residues: 555
  helix: -3.43 (0.64), residues: 34
  sheet:  1.24 (0.43), residues: 171
  loop : -0.80 (0.29), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.001   0.000   HIS H 101 
 PHE   0.011   0.001   PHE A 400 
 TYR   0.010   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
  89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A  503 VAL cc_start: 0.8405 (p) cc_final: 0.8001 (p)
REVERT: A  506 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8185 (mt0)
REVERT: B  444 LYS cc_start: 0.7298 (ttmm) cc_final: 0.6905 (tppt)
REVERT: L   42 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7912 (mtmt)
  outliers start: 7
  outliers final: 6
  residues processed: 87
  average time/residue: 1.2088
  time to fit residues: 109.3752
Evaluate side-chains
  86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
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 A residue  510 VAL
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.130128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.108231 restraints weight = 6395.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.91
r_work: 0.3207 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   4665  Z= 0.250
  Angle     :  0.626  12.043   6341  Z= 0.331
  Chirality :  0.046   0.168    659
  Planarity :  0.005   0.041    820
  Dihedral  :  4.470  20.614    635
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 21.38 %
    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 (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: -0.56 (0.34), residues: 555
  helix: -3.53 (0.64), residues: 34
  sheet:  1.16 (0.42), residues: 178
  loop : -0.91 (0.29), residues: 343

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   0.015   0.002   PHE B 338 
 TYR   0.021   0.002   TYR A 489 
 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: 4222.39 seconds
wall clock time: 75 minutes 9.18 seconds (4509.18 seconds total)