Starting phenix.real_space_refine
on Wed Mar  4 06:44:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wca_21604/03_2026/6wca_21604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wca_21604/03_2026/6wca_21604.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wca_21604/03_2026/6wca_21604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wca_21604/03_2026/6wca_21604.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wca_21604/03_2026/6wca_21604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wca_21604/03_2026/6wca_21604.map"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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: 6
    Type Number    sf(0)   Gaussians
     K       5      8.98       5
     S      38      5.16       5
     C    3758      2.51       5
     N     940      2.21       5
     O     994      1.98       5
     H    5910      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11645
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 5807
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 16, 'TRANS': 350}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 5807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 5807
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 16, 'TRANS': 350}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {'  K': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
  Time building chain proxies: 2.00, per 1000 atoms: 0.17
  Number of scatterers: 11645
  At special positions: 0
  Unit cell: (107.712, 68.544, 77.248, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     K       5     19.00
     S      38     16.00
     O     994      8.00
     N     940      7.00
     C    3758      6.00
     H    5910      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 346.0 milliseconds
  

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      88.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 50
    Processing helix  chain 'A' and resid 52 through 57
    Processing helix  chain 'A' and resid 61 through 65
    Processing helix  chain 'A' and resid 67 through 103
      removed outlier: 3.526A  pdb=" N   GLN A  71 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA A  75 " --> pdb=" O   GLN A  71 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL A 101 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLY A 103 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 122
      removed outlier: 3.643A  pdb=" N   PHE A 122 " --> pdb=" O   MET A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 133
      removed outlier: 4.242A  pdb=" N   THR A 132 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 164
      removed outlier: 3.545A  pdb=" N   PHE A 164 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 257 through 285
      removed outlier: 3.852A  pdb=" N   VAL A 285 " --> pdb=" O   CYS A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 295
    Processing helix  chain 'A' and resid 298 through 305
      removed outlier: 3.813A  pdb=" N   ALA A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 333
      removed outlier: 3.774A  pdb=" N   HIS A 333 " --> pdb=" O   SER A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 353
    Processing helix  chain 'A' and resid 354 through 359
    Processing helix  chain 'A' and resid 371 through 398
      removed outlier: 4.046A  pdb=" N   PHE A 389 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLN A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 405
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 415 through 440
      removed outlier: 5.047A  pdb=" N   TYR A 426 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
      Proline residue:  A 427  - end of helix
    Processing helix  chain 'A' and resid 443 through 461
      Proline residue:  A 456  - end of helix
    Processing helix  chain 'A' and resid 461 through 476
    Processing helix  chain 'B' and resid 33 through 50
    Processing helix  chain 'B' and resid 52 through 57
    Processing helix  chain 'B' and resid 61 through 65
    Processing helix  chain 'B' and resid 67 through 103
      removed outlier: 3.526A  pdb=" N   GLN B  71 " --> pdb=" O   ASP B  67 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA B  75 " --> pdb=" O   GLN B  71 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL B 101 " --> pdb=" O   ARG B  97 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY B 103 " --> pdb=" O   PHE B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 122
      removed outlier: 3.642A  pdb=" N   PHE B 122 " --> pdb=" O   MET B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 133
      removed outlier: 4.242A  pdb=" N   THR B 132 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE B 133 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 164
      removed outlier: 3.545A  pdb=" N   PHE B 164 " --> pdb=" O   TYR B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 168
    Processing helix  chain 'B' and resid 257 through 285
      removed outlier: 3.852A  pdb=" N   VAL B 285 " --> pdb=" O   CYS B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 295
    Processing helix  chain 'B' and resid 298 through 305
      removed outlier: 3.813A  pdb=" N   ALA B 302 " --> pdb=" O   SER B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 333
      removed outlier: 3.772A  pdb=" N   HIS B 333 " --> pdb=" O   SER B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 353
    Processing helix  chain 'B' and resid 354 through 359
    Processing helix  chain 'B' and resid 371 through 398
      removed outlier: 4.045A  pdb=" N   PHE B 389 " --> pdb=" O   LEU B 385 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLN B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 405
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 415 through 440
      removed outlier: 5.046A  pdb=" N   TYR B 426 " --> pdb=" O   LYS B 422 " (cutoff:3.500A)
      Proline residue:  B 427  - end of helix
    Processing helix  chain 'B' and resid 443 through 461
      Proline residue:  B 456  - end of helix
    Processing helix  chain 'B' and resid 461 through 476

    452 hydrogen bonds defined for protein.
    1326 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.13

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 5892
        1.03 -     1.22: 18
        1.22 -     1.42: 2386
        1.42 -     1.62: 3394
        1.62 -     1.81: 58
  Bond restraints: 11748
  Sorted by residual:
  bond pdb=" CA  VAL B 455 "
       pdb=" CB  VAL B 455 "
    ideal  model  delta    sigma   weight residual
    1.539  1.530  0.009 5.40e-03 3.43e+04 2.71e+00
  bond pdb=" CA  VAL A 455 "
       pdb=" CB  VAL A 455 "
    ideal  model  delta    sigma   weight residual
    1.539  1.530  0.009 5.40e-03 3.43e+04 2.54e+00
  bond pdb=" CB  ASP B 371 "
       pdb=" HB3 ASP B 371 "
    ideal  model  delta    sigma   weight residual
    0.970  1.001 -0.031 2.00e-02 2.50e+03 2.41e+00
  bond pdb=" CB  ASP B 371 "
       pdb=" HB2 ASP B 371 "
    ideal  model  delta    sigma   weight residual
    0.970  0.939  0.031 2.00e-02 2.50e+03 2.35e+00
  bond pdb=" CB  ASP B 279 "
       pdb=" CG  ASP B 279 "
    ideal  model  delta    sigma   weight residual
    1.516  1.548 -0.032 2.50e-02 1.60e+03 1.62e+00
  ... (remaining 11743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 20304
        1.28 -     2.56: 891
        2.56 -     3.85: 78
        3.85 -     5.13: 19
        5.13 -     6.41: 6
  Bond angle restraints: 21298
  Sorted by residual:
  angle pdb=" CA  ARG A 294 "
        pdb=" CB  ARG A 294 "
        pdb=" CG  ARG A 294 "
      ideal   model   delta    sigma   weight residual
     114.10  118.83   -4.73 2.00e+00 2.50e-01 5.59e+00
  angle pdb=" CA  ARG B 294 "
        pdb=" CB  ARG B 294 "
        pdb=" CG  ARG B 294 "
      ideal   model   delta    sigma   weight residual
     114.10  118.80   -4.70 2.00e+00 2.50e-01 5.53e+00
  angle pdb=" N   SER B 441 "
        pdb=" CA  SER B 441 "
        pdb=" CB  SER B 441 "
      ideal   model   delta    sigma   weight residual
     114.17  111.58    2.59 1.14e+00 7.69e-01 5.17e+00
  angle pdb=" N   SER A 441 "
        pdb=" CA  SER A 441 "
        pdb=" CB  SER A 441 "
      ideal   model   delta    sigma   weight residual
     114.17  111.60    2.57 1.14e+00 7.69e-01 5.08e+00
  angle pdb=" CG  ASP A 371 "
        pdb=" CB  ASP A 371 "
        pdb=" HB2 ASP A 371 "
      ideal   model   delta    sigma   weight residual
     108.00  114.41   -6.41 3.00e+00 1.11e-01 4.57e+00
  ... (remaining 21293 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 4787
       16.52 -    33.04: 548
       33.04 -    49.56: 127
       49.56 -    66.08: 58
       66.08 -    82.60: 10
  Dihedral angle restraints: 5530
    sinusoidal: 2938
      harmonic: 2592
  Sorted by residual:
  dihedral pdb=" CA  ASP A 283 "
           pdb=" C   ASP A 283 "
           pdb=" N   ASN A 284 "
           pdb=" CA  ASN A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.97  -25.03     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  ASP B 283 "
           pdb=" C   ASP B 283 "
           pdb=" N   ASN B 284 "
           pdb=" CA  ASN B 284 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.97  -25.03     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  ASP A 287 "
           pdb=" C   ASP A 287 "
           pdb=" N   PRO A 288 "
           pdb=" CA  PRO A 288 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.38  -21.62     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 5527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 636
       0.026 -    0.052: 179
       0.052 -    0.078: 108
       0.078 -    0.104: 40
       0.104 -    0.130: 15
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" CA  PRO B 288 "
            pdb=" N   PRO B 288 "
            pdb=" C   PRO B 288 "
            pdb=" CB  PRO B 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  PRO A 288 "
            pdb=" N   PRO A 288 "
            pdb=" C   PRO A 288 "
            pdb=" CB  PRO A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  PRO B  62 "
            pdb=" N   PRO B  62 "
            pdb=" C   PRO B  62 "
            pdb=" CB  PRO B  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 975 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 455 "   -0.031 5.00e-02 4.00e+02   4.69e-02 3.52e+00
        pdb=" N   PRO A 456 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 456 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 456 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 455 "    0.031 5.00e-02 4.00e+02   4.68e-02 3.50e+00
        pdb=" N   PRO B 456 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 456 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 456 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  53 "    0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO A  54 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A  54 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  54 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.30: 2189
        2.30 -     3.01: 32664
        3.01 -     3.72: 44616
        3.72 -     4.43: 65194
        4.43 -     5.14: 102460
  Nonbonded interactions: 247123
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 279 "
            pdb=" H   GLN B 361 "
     model   vdw
     1.592 2.450
  nonbonded pdb=" OD2 ASP A 279 "
            pdb=" H   GLN A 361 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" HG  SER A  61 "
            pdb=" OE1 GLU A  63 "
     model   vdw
     1.596 2.450
  nonbonded pdb=" HG  SER B  61 "
            pdb=" OE1 GLU B  63 "
     model   vdw
     1.641 2.450
  nonbonded pdb=" O   PHE B  85 "
            pdb=" HG1 THR B  89 "
     model   vdw
     1.643 2.450
  ... (remaining 247118 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 30 through 702)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.080
  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:             0.060
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.040
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
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   0.034   5838  Z= 0.160
  Angle     :  0.607   5.130   7956  Z= 0.342
  Chirality :  0.037   0.130    978
  Planarity :  0.004   0.047    976
  Dihedral  : 15.592  82.599   2040
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.77 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.30), residues: 726
  helix:  0.49 (0.21), residues: 584
  sheet:  None (None), residues: 0
  loop : -2.30 (0.50), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 294 
 TYR   0.016   0.002   TYR B 125 
 PHE   0.010   0.001   PHE A  99 
 TRP   0.008   0.001   TRP A 394 
 HIS   0.003   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5838)
  covalent geometry    : angle       0.60680 ( 7956)
  hydrogen bonds       : bond        0.11279 (  452)
  hydrogen bonds       : angle       5.10310 ( 1326)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 PHE cc_start: 0.8621 (m-80) cc_final: 0.8305 (m-80)
REVERT: A  282 GLU cc_start: 0.5093 (mm-30) cc_final: 0.3769 (mm-30)
REVERT: A  335 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7736 (mtp-110)
REVERT: B  142 LEU cc_start: 0.8401 (mt) cc_final: 0.8098 (tp)
REVERT: B  162 PHE cc_start: 0.8685 (m-80) cc_final: 0.8353 (m-80)
REVERT: B  282 GLU cc_start: 0.5079 (mm-30) cc_final: 0.3806 (mm-30)
REVERT: B  335 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7824 (mtp-110)
  outliers start: 12
  outliers final: 8
  residues processed: 113
  average time/residue: 0.1698
  time to fit residues: 25.1078
Evaluate side-chains
  99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain B residue   61 SER
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  303 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0270
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.8046

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

Flipped N/Q/H residues before XYZ refinement:
A 173 GLN
A 368 GLN
A 452 GLN
B 173 GLN
B 368 GLN
B 449 HIS
B 452 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.166279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.115170 restraints weight = 17861.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.20
r_work: 0.2992 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5838  Z= 0.199
  Angle     :  0.611   4.782   7956  Z= 0.323
  Chirality :  0.038   0.147    978
  Planarity :  0.005   0.049    976
  Dihedral  :  6.602  59.326    792
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.13 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.31), residues: 726
  helix:  1.63 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.10 (0.52), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 375 
 TYR   0.013   0.002   TYR B 313 
 PHE   0.017   0.002   PHE A  99 
 TRP   0.007   0.002   TRP A 394 
 HIS   0.006   0.002   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 5838)
  covalent geometry    : angle       0.61082 ( 7956)
  hydrogen bonds       : bond        0.06109 (  452)
  hydrogen bonds       : angle       4.16235 ( 1326)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  142 LEU cc_start: 0.8117 (mt) cc_final: 0.7890 (tp)
REVERT: A  162 PHE cc_start: 0.8810 (m-80) cc_final: 0.8313 (m-80)
REVERT: A  282 GLU cc_start: 0.5471 (mm-30) cc_final: 0.4177 (mm-30)
REVERT: A  336 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7927 (mtpp)
REVERT: B  142 LEU cc_start: 0.8249 (mt) cc_final: 0.8007 (tp)
REVERT: B  162 PHE cc_start: 0.8850 (m-80) cc_final: 0.8352 (m-80)
REVERT: B  282 GLU cc_start: 0.5326 (mm-30) cc_final: 0.4053 (mm-30)
REVERT: B  335 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7998 (mtp-110)
  outliers start: 15
  outliers final: 11
  residues processed: 107
  average time/residue: 0.1708
  time to fit residues: 24.1621
Evaluate side-chains
  101 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0970
   chunk 0 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 25 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 449 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.167737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.116547 restraints weight = 18106.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.20
r_work: 0.3001 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5838  Z= 0.162
  Angle     :  0.554   4.520   7956  Z= 0.287
  Chirality :  0.037   0.129    978
  Planarity :  0.005   0.048    976
  Dihedral  :  5.584  59.751    789
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.97 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.32), residues: 726
  helix:  2.15 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -1.78 (0.51), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 309 
 TYR   0.013   0.002   TYR A 313 
 PHE   0.016   0.001   PHE A  99 
 TRP   0.008   0.002   TRP A 394 
 HIS   0.004   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5838)
  covalent geometry    : angle       0.55351 ( 7956)
  hydrogen bonds       : bond        0.05518 (  452)
  hydrogen bonds       : angle       3.99298 ( 1326)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  162 PHE cc_start: 0.8849 (m-80) cc_final: 0.8342 (m-80)
REVERT: A  282 GLU cc_start: 0.5170 (mm-30) cc_final: 0.3954 (mm-30)
REVERT: A  336 LYS cc_start: 0.8255 (ttpp) cc_final: 0.7989 (mtpp)
REVERT: A  359 TYR cc_start: 0.8135 (m-80) cc_final: 0.7826 (m-10)
REVERT: B  282 GLU cc_start: 0.5160 (mm-30) cc_final: 0.3990 (mm-30)
REVERT: B  335 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7977 (mtp-110)
REVERT: B  359 TYR cc_start: 0.8228 (m-80) cc_final: 0.7838 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 103
  average time/residue: 0.1623
  time to fit residues: 22.1402
Evaluate side-chains
  95 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.165031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.113563 restraints weight = 18167.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.22
r_work: 0.2955 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5838  Z= 0.180
  Angle     :  0.560   4.482   7956  Z= 0.296
  Chirality :  0.037   0.130    978
  Planarity :  0.005   0.048    976
  Dihedral  :  5.336  57.797    788
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.81 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.31), residues: 726
  helix:  2.25 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -1.62 (0.51), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 294 
 TYR   0.013   0.002   TYR B 125 
 PHE   0.015   0.002   PHE B  99 
 TRP   0.008   0.002   TRP A 394 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 5838)
  covalent geometry    : angle       0.56018 ( 7956)
  hydrogen bonds       : bond        0.05514 (  452)
  hydrogen bonds       : angle       3.89785 ( 1326)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  162 PHE cc_start: 0.8899 (m-80) cc_final: 0.8371 (m-80)
REVERT: A  282 GLU cc_start: 0.5219 (mm-30) cc_final: 0.4129 (mm-30)
REVERT: B  282 GLU cc_start: 0.5190 (mm-30) cc_final: 0.4160 (mm-30)
REVERT: B  335 ARG cc_start: 0.8302 (mtp180) cc_final: 0.8084 (mtp-110)
REVERT: B  359 TYR cc_start: 0.8167 (m-80) cc_final: 0.7949 (m-10)
  outliers start: 17
  outliers final: 11
  residues processed: 105
  average time/residue: 0.1868
  time to fit residues: 25.1885
Evaluate side-chains
  97 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 69 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.166294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.115156 restraints weight = 18084.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.19
r_work: 0.3011 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5838  Z= 0.137
  Angle     :  0.524   4.715   7956  Z= 0.270
  Chirality :  0.036   0.119    978
  Planarity :  0.004   0.046    976
  Dihedral  :  5.161  55.534    788
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.29 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.32), residues: 726
  helix:  2.49 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -1.49 (0.52), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 294 
 TYR   0.015   0.002   TYR A 125 
 PHE   0.014   0.001   PHE B  99 
 TRP   0.009   0.001   TRP B 394 
 HIS   0.004   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5838)
  covalent geometry    : angle       0.52387 ( 7956)
  hydrogen bonds       : bond        0.04931 (  452)
  hydrogen bonds       : angle       3.80587 ( 1326)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  162 PHE cc_start: 0.8865 (m-80) cc_final: 0.8351 (m-80)
REVERT: A  169 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7359 (p)
REVERT: A  282 GLU cc_start: 0.4992 (mm-30) cc_final: 0.3968 (mm-30)
REVERT: B  282 GLU cc_start: 0.5014 (mm-30) cc_final: 0.4036 (mm-30)
REVERT: B  335 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8091 (mtp-110)
  outliers start: 12
  outliers final: 11
  residues processed: 99
  average time/residue: 0.1781
  time to fit residues: 23.0639
Evaluate side-chains
  97 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 69 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
B 452 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.162571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.109828 restraints weight = 18027.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.18
r_work: 0.2975 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5838  Z= 0.176
  Angle     :  0.543   4.459   7956  Z= 0.285
  Chirality :  0.037   0.124    978
  Planarity :  0.005   0.047    976
  Dihedral  :  5.121  54.107    788
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.29 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.71 (0.32), residues: 726
  helix:  2.42 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -1.48 (0.53), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 375 
 TYR   0.014   0.002   TYR B 125 
 PHE   0.014   0.002   PHE B  99 
 TRP   0.008   0.002   TRP A 394 
 HIS   0.006   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 5838)
  covalent geometry    : angle       0.54266 ( 7956)
  hydrogen bonds       : bond        0.05295 (  452)
  hydrogen bonds       : angle       3.82573 ( 1326)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  102 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8626 (tt)
REVERT: A  169 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.7411 (p)
REVERT: A  282 GLU cc_start: 0.5049 (mm-30) cc_final: 0.4058 (mm-30)
REVERT: B   43 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8626 (tt)
REVERT: B  169 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7394 (p)
REVERT: B  282 GLU cc_start: 0.5005 (mm-30) cc_final: 0.4077 (mm-30)
REVERT: B  335 ARG cc_start: 0.8284 (mtp180) cc_final: 0.8058 (mtp-110)
  outliers start: 17
  outliers final: 13
  residues processed: 102
  average time/residue: 0.1778
  time to fit residues: 23.4369
Evaluate side-chains
  99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.165125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.111917 restraints weight = 17863.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.24
r_work: 0.2962 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5838  Z= 0.132
  Angle     :  0.515   5.616   7956  Z= 0.264
  Chirality :  0.036   0.119    978
  Planarity :  0.004   0.045    976
  Dihedral  :  4.965  52.182    788
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.77 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.99 (0.32), residues: 726
  helix:  2.61 (0.21), residues: 602
  sheet:  None (None), residues: 0
  loop : -1.39 (0.54), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 474 
 TYR   0.016   0.002   TYR A 125 
 PHE   0.014   0.001   PHE B  99 
 TRP   0.009   0.001   TRP B 394 
 HIS   0.004   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5838)
  covalent geometry    : angle       0.51465 ( 7956)
  hydrogen bonds       : bond        0.04729 (  452)
  hydrogen bonds       : angle       3.72824 ( 1326)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6510 (tp)
REVERT: A  162 PHE cc_start: 0.8906 (m-80) cc_final: 0.8395 (m-80)
REVERT: A  169 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.7478 (p)
REVERT: A  282 GLU cc_start: 0.4910 (mm-30) cc_final: 0.3970 (mm-30)
REVERT: B   74 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6561 (tp)
REVERT: B  169 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.7396 (p)
REVERT: B  282 GLU cc_start: 0.4937 (mm-30) cc_final: 0.4045 (mm-30)
REVERT: B  335 ARG cc_start: 0.8347 (mtp180) cc_final: 0.8142 (mtp-110)
  outliers start: 14
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1706
  time to fit residues: 22.6503
Evaluate side-chains
  100 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 68 optimal weight:    8.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.3832 r_free = 0.3832 target = 0.163714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.111199 restraints weight = 17921.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.20
r_work: 0.2959 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5838  Z= 0.151
  Angle     :  0.525   4.697   7956  Z= 0.271
  Chirality :  0.036   0.121    978
  Planarity :  0.004   0.046    976
  Dihedral  :  4.918  51.452    788
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.61 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.90 (0.32), residues: 726
  helix:  2.54 (0.21), residues: 604
  sheet:  None (None), residues: 0
  loop : -1.48 (0.55), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 294 
 TYR   0.016   0.002   TYR A 125 
 PHE   0.014   0.001   PHE A  99 
 TRP   0.007   0.002   TRP A 324 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 5838)
  covalent geometry    : angle       0.52515 ( 7956)
  hydrogen bonds       : bond        0.04895 (  452)
  hydrogen bonds       : angle       3.73323 ( 1326)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8666 (tt)
REVERT: A   74 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6509 (tp)
REVERT: A  162 PHE cc_start: 0.8917 (m-80) cc_final: 0.8412 (m-80)
REVERT: A  169 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.7469 (p)
REVERT: A  282 GLU cc_start: 0.4915 (mm-30) cc_final: 0.3990 (mm-30)
REVERT: B   43 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8662 (tt)
REVERT: B   74 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6533 (tp)
REVERT: B  162 PHE cc_start: 0.8895 (m-80) cc_final: 0.8405 (m-80)
REVERT: B  169 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.7429 (p)
REVERT: B  282 GLU cc_start: 0.4833 (mm-30) cc_final: 0.3966 (mm-30)
REVERT: B  335 ARG cc_start: 0.8325 (mtp180) cc_final: 0.8076 (mtp-110)
  outliers start: 18
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1685
  time to fit residues: 23.5458
Evaluate side-chains
  108 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  122 PHE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0070
   chunk 33 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.1204

-------------------------------------------------------------------------------
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 = 0.3844 r_free = 0.3844 target = 0.165029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.112771 restraints weight = 17764.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.17
r_work: 0.2982 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2834 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5838  Z= 0.112
  Angle     :  0.500   5.064   7956  Z= 0.253
  Chirality :  0.035   0.117    978
  Planarity :  0.004   0.045    976
  Dihedral  :  4.778  49.779    788
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.94 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.21 (0.32), residues: 726
  helix:  2.76 (0.21), residues: 604
  sheet:  None (None), residues: 0
  loop : -1.40 (0.55), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 294 
 TYR   0.018   0.002   TYR B 125 
 PHE   0.012   0.001   PHE B  99 
 TRP   0.009   0.001   TRP B 394 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 5838)
  covalent geometry    : angle       0.50048 ( 7956)
  hydrogen bonds       : bond        0.04303 (  452)
  hydrogen bonds       : angle       3.62048 ( 1326)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6472 (tp)
REVERT: A  162 PHE cc_start: 0.8953 (m-80) cc_final: 0.8465 (m-80)
REVERT: A  282 GLU cc_start: 0.4843 (mm-30) cc_final: 0.3930 (mm-30)
REVERT: A  414 ARG cc_start: 0.7849 (mtp180) cc_final: 0.7632 (ttm110)
REVERT: B   74 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6465 (tp)
REVERT: B  162 PHE cc_start: 0.8910 (m-80) cc_final: 0.8419 (m-80)
REVERT: B  169 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.7426 (p)
REVERT: B  282 GLU cc_start: 0.4825 (mm-30) cc_final: 0.3959 (mm-30)
REVERT: B  335 ARG cc_start: 0.8340 (mtp180) cc_final: 0.8116 (mtp-110)
  outliers start: 15
  outliers final: 10
  residues processed: 108
  average time/residue: 0.2028
  time to fit residues: 27.8066
Evaluate side-chains
  103 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.161441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.108923 restraints weight = 18030.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.17
r_work: 0.2941 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5838  Z= 0.179
  Angle     :  0.550   5.343   7956  Z= 0.284
  Chirality :  0.037   0.124    978
  Planarity :  0.005   0.065    976
  Dihedral  :  4.847  49.270    788
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.97 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.91 (0.32), residues: 726
  helix:  2.54 (0.21), residues: 604
  sheet:  None (None), residues: 0
  loop : -1.44 (0.55), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 375 
 TYR   0.011   0.002   TYR A 359 
 PHE   0.016   0.001   PHE A  99 
 TRP   0.007   0.002   TRP A 324 
 HIS   0.006   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 5838)
  covalent geometry    : angle       0.54956 ( 7956)
  hydrogen bonds       : bond        0.05035 (  452)
  hydrogen bonds       : angle       3.71235 ( 1326)

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

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

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1452 Ramachandran restraints generated.
    726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  125 is missing expected H atoms. Skipping.
Residue TYR  125 is missing expected H atoms. Skipping.
Evaluate side-chains
  112 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6551 (tp)
REVERT: A  162 PHE cc_start: 0.8918 (m-80) cc_final: 0.8404 (m-80)
REVERT: A  169 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.7468 (p)
REVERT: A  282 GLU cc_start: 0.4849 (mm-30) cc_final: 0.3934 (mm-30)
REVERT: A  414 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7679 (ttm110)
REVERT: B   43 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8663 (tt)
REVERT: B   74 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6580 (tp)
REVERT: B  162 PHE cc_start: 0.8911 (m-80) cc_final: 0.8397 (m-80)
REVERT: B  169 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.7448 (p)
REVERT: B  282 GLU cc_start: 0.4802 (mm-30) cc_final: 0.3919 (mm-30)
REVERT: B  335 ARG cc_start: 0.8349 (mtp180) cc_final: 0.8098 (mtp-110)
  outliers start: 16
  outliers final: 11
  residues processed: 111
  average time/residue: 0.2241
  time to fit residues: 30.4735
Evaluate side-chains
  112 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  122 PHE
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  436 SER
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 29 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.165785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.113655 restraints weight = 17947.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.17
r_work: 0.3004 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5838  Z= 0.108
  Angle     :  0.510   5.294   7956  Z= 0.254
  Chirality :  0.035   0.116    978
  Planarity :  0.005   0.073    976
  Dihedral  :  4.688  47.251    788
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.77 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.32 (0.33), residues: 726
  helix:  2.83 (0.21), residues: 604
  sheet:  None (None), residues: 0
  loop : -1.35 (0.56), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 375 
 TYR   0.009   0.001   TYR B 125 
 PHE   0.009   0.001   PHE A  99 
 TRP   0.010   0.001   TRP B 394 
 HIS   0.003   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5838)
  covalent geometry    : angle       0.50963 ( 7956)
  hydrogen bonds       : bond        0.04128 (  452)
  hydrogen bonds       : angle       3.57800 ( 1326)

===============================================================================
Job complete
usr+sys time: 3177.07 seconds
wall clock time: 54 minutes 34.05 seconds (3274.05 seconds total)