Starting phenix.real_space_refine
on Wed Sep 17 21:23:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zxk_60542/09_2025/8zxk_60542.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zxk_60542/09_2025/8zxk_60542.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zxk_60542/09_2025/8zxk_60542.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zxk_60542/09_2025/8zxk_60542.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zxk_60542/09_2025/8zxk_60542.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zxk_60542/09_2025/8zxk_60542.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.047
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      48      5.16       5
     C    7844      2.51       5
     N    1794      2.21       5
     O    1967      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11653
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 495, 3866
          Classifications: {'peptide': 495}
          Link IDs: {'CIS': 3, 'PTRANS': 17, 'TRANS': 474}
    Chain: "B"
      Number of atoms: 3900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3900
          Classifications: {'peptide': 499}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 481}
    Chain: "C"
      Number of atoms: 3875
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 496, 3875
          Classifications: {'peptide': 496}
          Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 477}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'KEN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'KEN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'KEN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.89, per 1000 atoms: 0.25
  Number of scatterers: 11653
  At special positions: 0
  Unit cell: (111.3, 116.6, 79.5, 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      48     16.00
     O    1967      8.00
     N    1794      7.00
     C    7844      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 511.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2710

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 0 sheets defined
      84.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 35
      removed outlier: 5.266A  pdb=" N   THR A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 74
      removed outlier: 3.656A  pdb=" N   GLY A  40 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
      Proline residue:  A  44  - end of helix
      removed outlier: 5.741A  pdb=" N   TRP A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   PHE A  57 " --> pdb=" O   ASN A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 80
      removed outlier: 3.717A  pdb=" N   ARG A  79 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
      removed outlier: 3.645A  pdb=" N   ALA A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 113
      removed outlier: 3.659A  pdb=" N   MET A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 123
    Processing helix  chain 'A' and resid 130 through 147
    Processing helix  chain 'A' and resid 147 through 167
      removed outlier: 3.564A  pdb=" N   TRP A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 177
      No H-bonds generated for 'chain 'A' and resid 175 through 177'
    Processing helix  chain 'A' and resid 178 through 183
    Processing helix  chain 'A' and resid 190 through 226
      removed outlier: 3.883A  pdb=" N   ILE A 194 " --> pdb=" O   TRP A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 249
    Processing helix  chain 'A' and resid 262 through 279
    Processing helix  chain 'A' and resid 280 through 298
    Processing helix  chain 'A' and resid 298 through 304
    Processing helix  chain 'A' and resid 318 through 340
      Proline residue:  A 331  - end of helix
      removed outlier: 3.975A  pdb=" N   PHE A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE A 340 " --> pdb=" O   PHE A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 379
      removed outlier: 4.350A  pdb=" N   VAL A 356 " --> pdb=" O   GLY A 352 " (cutoff:3.500A)
      Proline residue:  A 357  - end of helix
      removed outlier: 3.987A  pdb=" N   SER A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 3.542A  pdb=" N   ALA A 385 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 400
    Processing helix  chain 'A' and resid 404 through 437
    Processing helix  chain 'A' and resid 443 through 464
      removed outlier: 4.172A  pdb=" N   ARG A 447 " --> pdb=" O   PRO A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 503
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'B' and resid 16 through 35
    Processing helix  chain 'B' and resid 35 through 74
      Proline residue:  B  44  - end of helix
      removed outlier: 5.701A  pdb=" N   TRP B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   PHE B  57 " --> pdb=" O   ASN B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 80
      removed outlier: 4.011A  pdb=" N   ARG B  79 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 101
    Processing helix  chain 'B' and resid 106 through 123
      removed outlier: 5.372A  pdb=" N   ILE B 114 " --> pdb=" O   MET B 110 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ALA B 115 " --> pdb=" O   PHE B 111 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLU B 116 " --> pdb=" O   PHE B 112 " (cutoff:3.500A)
      Proline residue:  B 117  - end of helix
    Processing helix  chain 'B' and resid 130 through 147
    Processing helix  chain 'B' and resid 147 through 167
      removed outlier: 3.614A  pdb=" N   TRP B 151 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 177
      No H-bonds generated for 'chain 'B' and resid 175 through 177'
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 190 through 226
      removed outlier: 3.720A  pdb=" N   ILE B 194 " --> pdb=" O   TRP B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 251
      removed outlier: 3.741A  pdb=" N   THR B 246 " --> pdb=" O   ILE B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 279
      removed outlier: 3.754A  pdb=" N   LYS B 258 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 298
    Processing helix  chain 'B' and resid 298 through 304
    Processing helix  chain 'B' and resid 313 through 317
    Processing helix  chain 'B' and resid 318 through 340
      Proline residue:  B 331  - end of helix
      removed outlier: 3.874A  pdb=" N   PHE B 336 " --> pdb=" O   PHE B 332 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B 340 " --> pdb=" O   PHE B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 379
      removed outlier: 4.364A  pdb=" N   VAL B 356 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
      Proline residue:  B 357  - end of helix
      removed outlier: 3.956A  pdb=" N   SER B 371 " --> pdb=" O   VAL B 367 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY B 379 " --> pdb=" O   THR B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 390
    Processing helix  chain 'B' and resid 393 through 400
    Processing helix  chain 'B' and resid 404 through 437
    Processing helix  chain 'B' and resid 443 through 464
      removed outlier: 3.942A  pdb=" N   ARG B 447 " --> pdb=" O   PRO B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 503
      Proline residue:  B 480  - end of helix
      removed outlier: 4.008A  pdb=" N   VAL B 483 " --> pdb=" O   LEU B 479 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   TYR B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 35
      removed outlier: 3.535A  pdb=" N   ILE C  19 " --> pdb=" O   PRO C  15 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   THR C  20 " --> pdb=" O   PRO C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 74
      removed outlier: 3.580A  pdb=" N   VAL C  41 " --> pdb=" O   GLU C  37 " (cutoff:3.500A)
      Proline residue:  C  44  - end of helix
      removed outlier: 5.694A  pdb=" N   TRP C  56 " --> pdb=" O   SER C  52 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   PHE C  57 " --> pdb=" O   ASN C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 80
      removed outlier: 3.859A  pdb=" N   ARG C  79 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 101
    Processing helix  chain 'C' and resid 106 through 113
    Processing helix  chain 'C' and resid 114 through 123
    Processing helix  chain 'C' and resid 130 through 147
    Processing helix  chain 'C' and resid 147 through 167
      removed outlier: 3.586A  pdb=" N   TRP C 151 " --> pdb=" O   GLY C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 186
      removed outlier: 3.526A  pdb=" N   PHE C 178 " --> pdb=" O   ARG C 175 " (cutoff:3.500A)
      Proline residue:  C 180  - end of helix
      removed outlier: 4.859A  pdb=" N   GLY C 183 " --> pdb=" O   PRO C 180 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   GLU C 184 " --> pdb=" O   PHE C 181 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ILE C 186 " --> pdb=" O   GLY C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 226
    Processing helix  chain 'C' and resid 230 through 251
      removed outlier: 3.979A  pdb=" N   SER C 248 " --> pdb=" O   ILE C 244 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL C 249 " --> pdb=" O   ALA C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 279
      removed outlier: 3.856A  pdb=" N   ASN C 262 " --> pdb=" O   LYS C 258 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET C 265 " --> pdb=" O   SER C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 298
    Processing helix  chain 'C' and resid 298 through 304
    Processing helix  chain 'C' and resid 318 through 340
      Proline residue:  C 331  - end of helix
      removed outlier: 4.244A  pdb=" N   SER C 335 " --> pdb=" O   PRO C 331 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE C 340 " --> pdb=" O   PHE C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 345 through 378
      removed outlier: 4.481A  pdb=" N   VAL C 356 " --> pdb=" O   GLY C 352 " (cutoff:3.500A)
      Proline residue:  C 357  - end of helix
      removed outlier: 3.977A  pdb=" N   SER C 371 " --> pdb=" O   VAL C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 390
    Processing helix  chain 'C' and resid 393 through 400
    Processing helix  chain 'C' and resid 404 through 437
    Processing helix  chain 'C' and resid 443 through 464
      removed outlier: 3.861A  pdb=" N   ARG C 447 " --> pdb=" O   PRO C 443 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 466 through 503
      Proline residue:  C 480  - end of helix

    916 hydrogen bonds defined for protein.
    2718 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: 1.96

  Time building geometry restraints manager: 1.43 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: 3400
        1.34 -     1.46: 2567
        1.46 -     1.57: 5950
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 12007
  Sorted by residual:
  bond pdb=" C   PRO C  15 "
       pdb=" N   PRO C  16 "
    ideal  model  delta    sigma   weight residual
    1.337  1.357 -0.020 1.24e-02 6.50e+03 2.48e+00
  bond pdb=" C   LEU B 479 "
       pdb=" N   PRO B 480 "
    ideal  model  delta    sigma   weight residual
    1.337  1.353 -0.016 1.24e-02 6.50e+03 1.71e+00
  bond pdb=" CB  ILE A 186 "
       pdb=" CG1 ILE A 186 "
    ideal  model  delta    sigma   weight residual
    1.530  1.556 -0.026 2.00e-02 2.50e+03 1.68e+00
  bond pdb=" NE1 KEN C 601 "
       pdb=" CC1 KEN C 601 "
    ideal  model  delta    sigma   weight residual
    1.445  1.469 -0.024 2.00e-02 2.50e+03 1.46e+00
  bond pdb=" NE1 KEN A 601 "
       pdb=" CA1 KEN A 601 "
    ideal  model  delta    sigma   weight residual
    1.446  1.470 -0.024 2.00e-02 2.50e+03 1.45e+00
  ... (remaining 12002 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 16219
        2.28 -     4.56: 130
        4.56 -     6.84: 28
        6.84 -     9.12: 2
        9.12 -    11.40: 2
  Bond angle restraints: 16381
  Sorted by residual:
  angle pdb=" C   GLU A 441 "
        pdb=" N   SER A 442 "
        pdb=" CA  SER A 442 "
      ideal   model   delta    sigma   weight residual
     121.70  133.10  -11.40 1.80e+00 3.09e-01 4.01e+01
  angle pdb=" C   LYS A 255 "
        pdb=" N   GLY A 256 "
        pdb=" CA  GLY A 256 "
      ideal   model   delta    sigma   weight residual
     121.70  131.54   -9.84 1.80e+00 3.09e-01 2.99e+01
  angle pdb=" CB  ILE A 186 "
        pdb=" CG1 ILE A 186 "
        pdb=" CD1 ILE A 186 "
      ideal   model   delta    sigma   weight residual
     113.80  122.02   -8.22 2.10e+00 2.27e-01 1.53e+01
  angle pdb=" N   ILE B 186 "
        pdb=" CA  ILE B 186 "
        pdb=" C   ILE B 186 "
      ideal   model   delta    sigma   weight residual
     106.21  110.27   -4.06 1.07e+00 8.73e-01 1.44e+01
  angle pdb=" CA  TRP B 329 "
        pdb=" CB  TRP B 329 "
        pdb=" CG  TRP B 329 "
      ideal   model   delta    sigma   weight residual
     113.60  120.20   -6.60 1.90e+00 2.77e-01 1.21e+01
  ... (remaining 16376 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 5795
       17.80 -    35.59: 705
       35.59 -    53.39: 158
       53.39 -    71.18: 24
       71.18 -    88.98: 12
  Dihedral angle restraints: 6694
    sinusoidal: 2464
      harmonic: 4230
  Sorted by residual:
  dihedral pdb=" CA  THR B 103 "
           pdb=" C   THR B 103 "
           pdb=" N   GLY B 104 "
           pdb=" CA  GLY B 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.90   18.10     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CB  GLU A  37 "
           pdb=" CG  GLU A  37 "
           pdb=" CD  GLU A  37 "
           pdb=" OE1 GLU A  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.98  -88.98     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CA  TRP C 323 "
           pdb=" CB  TRP C 323 "
           pdb=" CG  TRP C 323 "
           pdb=" CD1 TRP C 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  159.01  -69.01     2      2.00e+01 2.50e-03 1.05e+01
  ... (remaining 6691 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1270
       0.034 -    0.068: 460
       0.068 -    0.101: 135
       0.101 -    0.135: 20
       0.135 -    0.169: 4
  Chirality restraints: 1889
  Sorted by residual:
  chirality pdb=" CG  LEU C  23 "
            pdb=" CB  LEU C  23 "
            pdb=" CD1 LEU C  23 "
            pdb=" CD2 LEU C  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" CB  ILE A 186 "
            pdb=" CA  ILE A 186 "
            pdb=" CG1 ILE A 186 "
            pdb=" CG2 ILE A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.98e-01
  chirality pdb=" CA  LEU C  23 "
            pdb=" N   LEU C  23 "
            pdb=" C   LEU C  23 "
            pdb=" CB  LEU C  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.95e-01
  ... (remaining 1886 not shown)

  Planarity restraints: 1975
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  14 "    0.036 5.00e-02 4.00e+02   5.53e-02 4.90e+00
        pdb=" N   PRO A  15 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A  15 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  15 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 366 "   -0.011 2.00e-02 2.50e+03   2.12e-02 4.51e+00
        pdb=" C   ASN A 366 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ASN A 366 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   VAL A 367 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 366 "    0.010 2.00e-02 2.50e+03   1.94e-02 3.77e+00
        pdb=" C   ASN C 366 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ASN C 366 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL C 367 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1972 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 339
        2.72 -     3.26: 12099
        3.26 -     3.81: 20987
        3.81 -     4.35: 24860
        4.35 -     4.90: 43652
  Nonbonded interactions: 101937
  Sorted by model distance:
  nonbonded pdb=" O   SER C 341 "
            pdb=" OG  SER C 341 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" O   PHE A 299 "
            pdb=" OG  SER A 303 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   PHE C 299 "
            pdb=" OG  SER C 303 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   LEU C 177 "
            pdb=" OG  SER C 491 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OE1 GLN B  47 "
            pdb=" OG1 THR B 472 "
     model   vdw
     2.246 3.040
  ... (remaining 101932 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'
  selection = (chain 'B' and (resid 10 through 504 or resid 601))
  selection = (chain 'C' and (resid 10 through 504 or resid 601))
}

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:             1.060
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.040
  Find NCS groups from input model:        0.250
  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:6.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
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   0.037  12009  Z= 0.137
  Angle     :  0.543  11.395  16381  Z= 0.299
  Chirality :  0.038   0.169   1889
  Planarity :  0.004   0.055   1975
  Dihedral  : 16.405  88.978   3984
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 24.98 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.22), residues: 1484
  helix:  2.15 (0.15), residues: 1167
  sheet:  None (None), residues: 0
  loop : -0.25 (0.37), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 344 
 TYR   0.008   0.001   TYR A 295 
 PHE   0.022   0.002   PHE B 417 
 TRP   0.027   0.001   TRP B 329 
 HIS   0.002   0.001   HIS C 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (12007)
  covalent geometry    : angle       0.54288 (16381)
  hydrogen bonds       : bond        0.09754 (  916)
  hydrogen bonds       : angle       5.53498 ( 2718)
  Misc. bond           : bond        0.00051 (    2)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 145
  time to evaluate  : 0.439 
Fit side-chains
REVERT: B   19 ILE cc_start: 0.7971 (mm) cc_final: 0.7745 (mp)
REVERT: B  105 MET cc_start: 0.2930 (mmm) cc_final: 0.2602 (mpp)
REVERT: C   93 LYS cc_start: 0.4598 (pttp) cc_final: 0.4094 (ptpt)
  outliers start: 2
  outliers final: 0
  residues processed: 147
  average time/residue: 0.4352
  time to fit residues: 71.5837
Evaluate side-chains
  139 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 446 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.157649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.114108 restraints weight = 12428.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.97
r_work: 0.2975 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.0652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12009  Z= 0.177
  Angle     :  0.545   7.657  16381  Z= 0.298
  Chirality :  0.040   0.153   1889
  Planarity :  0.004   0.049   1975
  Dihedral  :  4.084  17.510   1547
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 20.99 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.22), residues: 1484
  helix:  2.04 (0.15), residues: 1180
  sheet:  None (None), residues: 0
  loop : -0.06 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 168 
 TYR   0.010   0.001   TYR C 490 
 PHE   0.025   0.002   PHE B 122 
 TRP   0.033   0.001   TRP B 329 
 HIS   0.003   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (12007)
  covalent geometry    : angle       0.54501 (16381)
  hydrogen bonds       : bond        0.04782 (  916)
  hydrogen bonds       : angle       4.82293 ( 2718)
  Misc. bond           : bond        0.00049 (    2)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 140
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A   93 LYS cc_start: 0.3854 (OUTLIER) cc_final: 0.3405 (ttpt)
REVERT: A  181 PHE cc_start: 0.7750 (m-10) cc_final: 0.7516 (m-10)
REVERT: A  184 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6614 (mm-30)
REVERT: B   19 ILE cc_start: 0.7083 (mm) cc_final: 0.6628 (mp)
REVERT: B   93 LYS cc_start: 0.3477 (OUTLIER) cc_final: 0.3186 (ttpt)
  outliers start: 57
  outliers final: 19
  residues processed: 183
  average time/residue: 0.3582
  time to fit residues: 74.7254
Evaluate side-chains
  160 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain A residue  323 TRP
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 TRP
Chi-restraints excluded: chain B residue  392 SER
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  323 TRP
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  488 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 96 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0000
   chunk 51 optimal weight:    3.9990
   chunk 108 optimal weight:    0.7980
   chunk 135 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** C 192 HIS ** 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 = 0.3771 r_free = 0.3771 target = 0.159478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.115608 restraints weight = 12519.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.96
r_work: 0.3014 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.0682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12009  Z= 0.135
  Angle     :  0.514   6.799  16381  Z= 0.279
  Chirality :  0.038   0.145   1889
  Planarity :  0.004   0.047   1975
  Dihedral  :  4.017  18.083   1547
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 21.64 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.22), residues: 1484
  helix:  2.19 (0.15), residues: 1175
  sheet:  None (None), residues: 0
  loop : -0.20 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 168 
 TYR   0.008   0.001   TYR A 295 
 PHE   0.022   0.002   PHE B 122 
 TRP   0.029   0.001   TRP B 329 
 HIS   0.002   0.001   HIS C 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (12007)
  covalent geometry    : angle       0.51420 (16381)
  hydrogen bonds       : bond        0.04410 (  916)
  hydrogen bonds       : angle       4.63480 ( 2718)
  Misc. bond           : bond        0.00031 (    2)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 146
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A   93 LYS cc_start: 0.3834 (OUTLIER) cc_final: 0.3388 (ttpt)
REVERT: A  123 ASN cc_start: 0.8249 (t0) cc_final: 0.7925 (t0)
REVERT: A  181 PHE cc_start: 0.7647 (m-10) cc_final: 0.7293 (m-10)
REVERT: A  184 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6509 (mm-30)
REVERT: A  265 MET cc_start: 0.7643 (mmp) cc_final: 0.5939 (ttp)
REVERT: B   19 ILE cc_start: 0.7167 (mm) cc_final: 0.6725 (mp)
REVERT: B   93 LYS cc_start: 0.3449 (OUTLIER) cc_final: 0.3134 (ttpt)
REVERT: B  336 PHE cc_start: 0.7783 (m-80) cc_final: 0.7551 (m-80)
REVERT: C  126 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7661 (mtm180)
REVERT: C  301 ASP cc_start: 0.7909 (t0) cc_final: 0.7583 (t0)
  outliers start: 49
  outliers final: 19
  residues processed: 182
  average time/residue: 0.3905
  time to fit residues: 80.2847
Evaluate side-chains
  163 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain B residue   13 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  126 ARG
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  432 ASP
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  488 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 144 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 135 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 146 optimal weight:    3.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 123 ASN
C 140 GLN
** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.157136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.104463 restraints weight = 12519.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 1.73
r_work: 0.2967 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.0868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12009  Z= 0.184
  Angle     :  0.555   8.475  16381  Z= 0.300
  Chirality :  0.040   0.152   1889
  Planarity :  0.004   0.045   1975
  Dihedral  :  4.108  16.211   1547
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 20.42 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.22), residues: 1484
  helix:  1.99 (0.15), residues: 1178
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 344 
 TYR   0.012   0.001   TYR C 490 
 PHE   0.027   0.002   PHE B 417 
 TRP   0.036   0.001   TRP B 329 
 HIS   0.002   0.001   HIS C 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (12007)
  covalent geometry    : angle       0.55470 (16381)
  hydrogen bonds       : bond        0.04819 (  916)
  hydrogen bonds       : angle       4.70105 ( 2718)
  Misc. bond           : bond        0.00053 (    2)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 141
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A   93 LYS cc_start: 0.4057 (OUTLIER) cc_final: 0.3591 (ttpt)
REVERT: A  105 MET cc_start: 0.6258 (tmm) cc_final: 0.5991 (tmm)
REVERT: A  181 PHE cc_start: 0.7854 (m-10) cc_final: 0.7436 (m-10)
REVERT: A  184 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6644 (mm-30)
REVERT: A  265 MET cc_start: 0.7889 (mmp) cc_final: 0.6262 (ttp)
REVERT: A  329 TRP cc_start: 0.7290 (OUTLIER) cc_final: 0.6920 (t60)
REVERT: B   19 ILE cc_start: 0.7485 (mm) cc_final: 0.7017 (mp)
REVERT: B   93 LYS cc_start: 0.3658 (OUTLIER) cc_final: 0.3333 (ttpt)
REVERT: C   23 LEU cc_start: 0.7759 (mm) cc_final: 0.7427 (mm)
REVERT: C  126 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7855 (mtm180)
REVERT: C  301 ASP cc_start: 0.7998 (t0) cc_final: 0.7692 (t0)
  outliers start: 65
  outliers final: 35
  residues processed: 190
  average time/residue: 0.3580
  time to fit residues: 77.0414
Evaluate side-chains
  178 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 138
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 TRP
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain B residue   13 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 TRP
Chi-restraints excluded: chain B residue  392 SER
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  126 ARG
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  323 TRP
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  392 SER
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  432 ASP
Chi-restraints excluded: chain C residue  474 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  488 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 126 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 73 optimal weight:   10.0000
   chunk 54 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 7 optimal weight:    0.4980
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 123 ASN
** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.159571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.115020 restraints weight = 12426.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.98
r_work: 0.3006 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.0813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12009  Z= 0.134
  Angle     :  0.516   7.338  16381  Z= 0.280
  Chirality :  0.038   0.172   1889
  Planarity :  0.004   0.045   1975
  Dihedral  :  4.025  18.102   1547
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 21.07 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.57 (0.22), residues: 1484
  helix:  2.19 (0.15), residues: 1175
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 168 
 TYR   0.008   0.001   TYR A 295 
 PHE   0.021   0.002   PHE B 122 
 TRP   0.032   0.001   TRP B 329 
 HIS   0.002   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (12007)
  covalent geometry    : angle       0.51598 (16381)
  hydrogen bonds       : bond        0.04385 (  916)
  hydrogen bonds       : angle       4.55708 ( 2718)
  Misc. bond           : bond        0.00027 (    2)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 146
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A   93 LYS cc_start: 0.3849 (OUTLIER) cc_final: 0.3381 (ttpt)
REVERT: A  123 ASN cc_start: 0.8334 (t0) cc_final: 0.8002 (t0)
REVERT: A  265 MET cc_start: 0.7771 (mmp) cc_final: 0.6092 (tmm)
REVERT: B   19 ILE cc_start: 0.7098 (mm) cc_final: 0.6648 (mp)
REVERT: B   93 LYS cc_start: 0.3467 (OUTLIER) cc_final: 0.3142 (ttpt)
REVERT: B  502 LYS cc_start: 0.6550 (ttpt) cc_final: 0.5811 (ttpp)
REVERT: C   23 LEU cc_start: 0.7753 (mm) cc_final: 0.7396 (mm)
REVERT: C  126 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7755 (mtm180)
REVERT: C  301 ASP cc_start: 0.7943 (t0) cc_final: 0.7609 (t0)
  outliers start: 67
  outliers final: 35
  residues processed: 196
  average time/residue: 0.3689
  time to fit residues: 82.1030
Evaluate side-chains
  180 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 142
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 TRP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain B residue   13 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  126 ARG
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  250 PHE
Chi-restraints excluded: chain C residue  323 TRP
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  392 SER
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  474 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  488 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 136 optimal weight:    0.6980
   chunk 143 optimal weight:    5.9990
   chunk 107 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 123 optimal weight:    0.7980
   chunk 131 optimal weight:    0.0770
   chunk 138 optimal weight:    0.5980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
B  14 ASN
B 454 GLN
C 123 ASN
** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.160478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.116544 restraints weight = 12449.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.96
r_work: 0.3015 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.0897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12009  Z= 0.128
  Angle     :  0.526   9.993  16381  Z= 0.281
  Chirality :  0.038   0.162   1889
  Planarity :  0.004   0.044   1975
  Dihedral  :  3.957  15.965   1547
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 22.46 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.22), residues: 1484
  helix:  2.29 (0.15), residues: 1174
  sheet:  None (None), residues: 0
  loop : -0.19 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 168 
 TYR   0.008   0.001   TYR A 295 
 PHE   0.026   0.002   PHE B 417 
 TRP   0.031   0.001   TRP B 329 
 HIS   0.002   0.001   HIS C 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (12007)
  covalent geometry    : angle       0.52639 (16381)
  hydrogen bonds       : bond        0.04259 (  916)
  hydrogen bonds       : angle       4.48253 ( 2718)
  Misc. bond           : bond        0.00037 (    2)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 148
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A   93 LYS cc_start: 0.3574 (OUTLIER) cc_final: 0.3123 (ttpt)
REVERT: A  123 ASN cc_start: 0.8345 (t0) cc_final: 0.8029 (t0)
REVERT: A  265 MET cc_start: 0.7620 (mmp) cc_final: 0.5906 (ttt)
REVERT: A  336 PHE cc_start: 0.7653 (m-80) cc_final: 0.7339 (m-80)
REVERT: B   19 ILE cc_start: 0.6925 (mm) cc_final: 0.6498 (mp)
REVERT: B   43 PHE cc_start: 0.5694 (m-10) cc_final: 0.5366 (m-10)
REVERT: B  502 LYS cc_start: 0.6496 (ttpt) cc_final: 0.5764 (ttpp)
REVERT: C   23 LEU cc_start: 0.7690 (mm) cc_final: 0.7328 (mm)
REVERT: C   35 PHE cc_start: 0.7087 (m-10) cc_final: 0.6765 (m-10)
REVERT: C  126 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7639 (mtm180)
REVERT: C  258 LYS cc_start: 0.4483 (OUTLIER) cc_final: 0.3677 (mmtt)
  outliers start: 59
  outliers final: 36
  residues processed: 193
  average time/residue: 0.3703
  time to fit residues: 81.1616
Evaluate side-chains
  182 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 143
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  323 TRP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  488 MET
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain B residue   13 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 TRP
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  126 ARG
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  250 PHE
Chi-restraints excluded: chain C residue  258 LYS
Chi-restraints excluded: chain C residue  323 TRP
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  432 ASP
Chi-restraints excluded: chain C residue  474 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  488 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   chunk 61 optimal weight:    0.2980
   chunk 72 optimal weight:    0.9990
   chunk 120 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0870
   chunk 127 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
C 123 ASN
** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.160492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.116374 restraints weight = 12438.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.97
r_work: 0.3005 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12009  Z= 0.132
  Angle     :  0.523  10.341  16381  Z= 0.280
  Chirality :  0.038   0.155   1889
  Planarity :  0.004   0.043   1975
  Dihedral  :  3.942  16.022   1547
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 22.21 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.22), residues: 1484
  helix:  2.28 (0.15), residues: 1174
  sheet:  None (None), residues: 0
  loop : -0.20 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 168 
 TYR   0.008   0.001   TYR A 295 
 PHE   0.022   0.002   PHE B 122 
 TRP   0.030   0.001   TRP B 329 
 HIS   0.002   0.001   HIS C 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (12007)
  covalent geometry    : angle       0.52330 (16381)
  hydrogen bonds       : bond        0.04279 (  916)
  hydrogen bonds       : angle       4.46873 ( 2718)
  Misc. bond           : bond        0.00020 (    2)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 149
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   93 LYS cc_start: 0.3688 (OUTLIER) cc_final: 0.3232 (ttpt)
REVERT: A  123 ASN cc_start: 0.8290 (t0) cc_final: 0.7978 (t0)
REVERT: A  184 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6420 (mm-30)
REVERT: A  265 MET cc_start: 0.7623 (mmp) cc_final: 0.5917 (ttt)
REVERT: B   19 ILE cc_start: 0.6923 (mm) cc_final: 0.6507 (mp)
REVERT: B   43 PHE cc_start: 0.5691 (m-10) cc_final: 0.5360 (m-10)
REVERT: B   93 LYS cc_start: 0.3334 (OUTLIER) cc_final: 0.3010 (ttpt)
REVERT: B  502 LYS cc_start: 0.6453 (ttpt) cc_final: 0.5739 (ttpp)
REVERT: C   23 LEU cc_start: 0.7622 (mm) cc_final: 0.7246 (mm)
REVERT: C  126 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7623 (mtm180)
REVERT: C  258 LYS cc_start: 0.4486 (OUTLIER) cc_final: 0.3677 (mmtt)
  outliers start: 63
  outliers final: 36
  residues processed: 198
  average time/residue: 0.3614
  time to fit residues: 81.2322
Evaluate side-chains
  186 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 145
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  323 TRP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  488 MET
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain B residue   13 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 TRP
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  126 ARG
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  250 PHE
Chi-restraints excluded: chain C residue  258 LYS
Chi-restraints excluded: chain C residue  323 TRP
Chi-restraints excluded: chain C residue  392 SER
Chi-restraints excluded: chain C residue  432 ASP
Chi-restraints excluded: chain C residue  474 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  488 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 112 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 123 ASN
** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.157399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.104846 restraints weight = 12450.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 1.71
r_work: 0.2969 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12009  Z= 0.184
  Angle     :  0.568  11.247  16381  Z= 0.306
  Chirality :  0.041   0.169   1889
  Planarity :  0.004   0.044   1975
  Dihedral  :  4.090  16.324   1547
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 22.70 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.22), residues: 1484
  helix:  2.02 (0.14), residues: 1178
  sheet:  None (None), residues: 0
  loop : -0.21 (0.40), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 168 
 TYR   0.012   0.001   TYR C 490 
 PHE   0.030   0.002   PHE B 417 
 TRP   0.034   0.002   TRP B 329 
 HIS   0.003   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (12007)
  covalent geometry    : angle       0.56822 (16381)
  hydrogen bonds       : bond        0.04785 (  916)
  hydrogen bonds       : angle       4.62942 ( 2718)
  Misc. bond           : bond        0.00040 (    2)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 138
  time to evaluate  : 0.447 
Fit side-chains
REVERT: A   93 LYS cc_start: 0.3955 (OUTLIER) cc_final: 0.3501 (ttpt)
REVERT: A  265 MET cc_start: 0.7868 (mmp) cc_final: 0.6245 (ttt)
REVERT: A  329 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.6732 (t60)
REVERT: B   19 ILE cc_start: 0.7192 (mm) cc_final: 0.6738 (mp)
REVERT: B   93 LYS cc_start: 0.3570 (OUTLIER) cc_final: 0.3267 (ttpt)
REVERT: B  105 MET cc_start: 0.2086 (mmt) cc_final: 0.1874 (mmp)
REVERT: C   23 LEU cc_start: 0.7720 (mm) cc_final: 0.7299 (mm)
REVERT: C   48 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8021 (tm)
REVERT: C  126 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7842 (mtm180)
REVERT: C  258 LYS cc_start: 0.4698 (OUTLIER) cc_final: 0.3859 (mmtt)
REVERT: C  301 ASP cc_start: 0.8000 (t0) cc_final: 0.7674 (t0)
  outliers start: 59
  outliers final: 41
  residues processed: 184
  average time/residue: 0.3634
  time to fit residues: 75.7882
Evaluate side-chains
  185 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 138
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 TRP
Chi-restraints excluded: chain A residue  329 TRP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain B residue   13 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 TRP
Chi-restraints excluded: chain B residue  392 SER
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  126 ARG
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  250 PHE
Chi-restraints excluded: chain C residue  258 LYS
Chi-restraints excluded: chain C residue  323 TRP
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  392 SER
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  432 ASP
Chi-restraints excluded: chain C residue  474 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  488 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 136 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 137 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0870
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
C 123 ASN
** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.160064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.116204 restraints weight = 12326.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 1.94
r_work: 0.3000 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.0970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12009  Z= 0.135
  Angle     :  0.534  12.283  16381  Z= 0.287
  Chirality :  0.039   0.146   1889
  Planarity :  0.004   0.044   1975
  Dihedral  :  4.003  16.454   1547
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 23.84 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.22), residues: 1484
  helix:  2.19 (0.15), residues: 1177
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 168 
 TYR   0.008   0.001   TYR A 295 
 PHE   0.021   0.002   PHE B 122 
 TRP   0.031   0.001   TRP C 445 
 HIS   0.002   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (12007)
  covalent geometry    : angle       0.53423 (16381)
  hydrogen bonds       : bond        0.04336 (  916)
  hydrogen bonds       : angle       4.50469 ( 2718)
  Misc. bond           : bond        0.00020 (    2)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 142
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LYS cc_start: 0.3818 (OUTLIER) cc_final: 0.3365 (ttpt)
REVERT: A  123 ASN cc_start: 0.8250 (t0) cc_final: 0.7933 (t0)
REVERT: A  265 MET cc_start: 0.7635 (mmp) cc_final: 0.5944 (ttt)
REVERT: B   19 ILE cc_start: 0.6939 (mm) cc_final: 0.6521 (mp)
REVERT: B   93 LYS cc_start: 0.3400 (OUTLIER) cc_final: 0.3079 (ttpt)
REVERT: B  105 MET cc_start: 0.2292 (mmt) cc_final: 0.1819 (mmp)
REVERT: C   35 PHE cc_start: 0.7094 (m-10) cc_final: 0.6793 (m-10)
REVERT: C  126 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7670 (mtm180)
REVERT: C  417 PHE cc_start: 0.7488 (t80) cc_final: 0.7217 (t80)
  outliers start: 49
  outliers final: 40
  residues processed: 180
  average time/residue: 0.3688
  time to fit residues: 75.4816
Evaluate side-chains
  183 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 140
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 TRP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  488 MET
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain B residue   13 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 TRP
Chi-restraints excluded: chain B residue  392 SER
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  126 ARG
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  250 PHE
Chi-restraints excluded: chain C residue  323 TRP
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  392 SER
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  432 ASP
Chi-restraints excluded: chain C residue  474 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  488 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 32 optimal weight:    0.3980
   chunk 60 optimal weight:    0.3980
   chunk 36 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
C 123 ASN
** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.159225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.114899 restraints weight = 12497.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.96
r_work: 0.3007 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.0993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12009  Z= 0.150
  Angle     :  0.545  11.633  16381  Z= 0.293
  Chirality :  0.039   0.148   1889
  Planarity :  0.004   0.044   1975
  Dihedral  :  4.020  16.084   1547
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 24.41 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.51 (0.22), residues: 1484
  helix:  2.14 (0.15), residues: 1178
  sheet:  None (None), residues: 0
  loop : -0.19 (0.39), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 168 
 TYR   0.009   0.001   TYR C 490 
 PHE   0.028   0.002   PHE B 417 
 TRP   0.033   0.001   TRP C 445 
 HIS   0.002   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (12007)
  covalent geometry    : angle       0.54523 (16381)
  hydrogen bonds       : bond        0.04477 (  916)
  hydrogen bonds       : angle       4.53037 ( 2718)
  Misc. bond           : bond        0.00041 (    2)

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

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

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2968 Ramachandran restraints generated.
    1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 139
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 LYS cc_start: 0.3742 (OUTLIER) cc_final: 0.3281 (ttpt)
REVERT: A  123 ASN cc_start: 0.8381 (t0) cc_final: 0.8044 (t0)
REVERT: A  265 MET cc_start: 0.7654 (mmp) cc_final: 0.5958 (ttt)
REVERT: B   19 ILE cc_start: 0.6910 (mm) cc_final: 0.6482 (mp)
REVERT: B   93 LYS cc_start: 0.3398 (OUTLIER) cc_final: 0.3087 (ttpt)
REVERT: B  105 MET cc_start: 0.2410 (mmt) cc_final: 0.1832 (mmp)
REVERT: C  126 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7682 (mtm180)
REVERT: C  417 PHE cc_start: 0.7508 (t80) cc_final: 0.7230 (t80)
  outliers start: 44
  outliers final: 38
  residues processed: 175
  average time/residue: 0.3652
  time to fit residues: 72.5778
Evaluate side-chains
  179 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 138
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  323 TRP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  499 GLU
Chi-restraints excluded: chain B residue   13 ILE
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  174 PHE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  323 TRP
Chi-restraints excluded: chain B residue  392 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  126 ARG
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  250 PHE
Chi-restraints excluded: chain C residue  323 TRP
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  392 SER
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  432 ASP
Chi-restraints excluded: chain C residue  474 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  488 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 134 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 129 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
C 123 ASN
** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.159445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.114508 restraints weight = 12472.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.00
r_work: 0.3004 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12009  Z= 0.147
  Angle     :  0.544  11.298  16381  Z= 0.293
  Chirality :  0.039   0.154   1889
  Planarity :  0.004   0.044   1975
  Dihedral  :  4.026  17.021   1547
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 24.49 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (0.22), residues: 1484
  helix:  2.16 (0.15), residues: 1175
  sheet:  None (None), residues: 0
  loop : -0.23 (0.39), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 168 
 TYR   0.009   0.001   TYR C 490 
 PHE   0.024   0.002   PHE A 417 
 TRP   0.032   0.001   TRP C 445 
 HIS   0.002   0.001   HIS C 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (12007)
  covalent geometry    : angle       0.54359 (16381)
  hydrogen bonds       : bond        0.04449 (  916)
  hydrogen bonds       : angle       4.53205 ( 2718)
  Misc. bond           : bond        0.00025 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3795.47 seconds
wall clock time: 65 minutes 30.02 seconds (3930.02 seconds total)