Starting phenix.real_space_refine
on Sun Apr 27 13:25:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tgk_41239/04_2025/8tgk_41239_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tgk_41239/04_2025/8tgk_41239.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tgk_41239/04_2025/8tgk_41239.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tgk_41239/04_2025/8tgk_41239.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tgk_41239/04_2025/8tgk_41239_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tgk_41239/04_2025/8tgk_41239_trim.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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      57      5.16       5
     C    3837      2.51       5
     N     900      2.21       5
     O     978      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5772
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2864
          Classifications: {'peptide': 384}
          Link IDs: {'PTRANS': 23, 'TRANS': 360}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2856
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 21, 'TRANS': 360}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'HSM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'YHR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.92, per 1000 atoms: 0.85
  Number of scatterers: 5772
  At special positions: 0
  Unit cell: (72.5973, 63.744, 114.208, 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      57     16.00
     O     978      8.00
     N     900      7.00
     C    3837      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=0, symmetry=0
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 875.6 milliseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1370

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      91.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 41
      removed outlier: 3.839A  pdb=" N   LEU A  24 " --> pdb=" O   ARG A  20 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL A  25 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   PHE A  38 " --> pdb=" O   ASP A  34 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   VAL A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 51
      removed outlier: 3.789A  pdb=" N   TYR A  50 " --> pdb=" O   PRO A  46 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP A  51 " --> pdb=" O   THR A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 144
      removed outlier: 3.550A  pdb=" N   LEU A 142 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   PHE A 143 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 158
      removed outlier: 3.502A  pdb=" N   MET A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      Proline residue:  A 155  - end of helix
    Processing helix  chain 'A' and resid 159 through 165
      removed outlier: 4.030A  pdb=" N   ARG A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 187
    Processing helix  chain 'A' and resid 190 through 193
    Processing helix  chain 'A' and resid 194 through 219
    Processing helix  chain 'A' and resid 221 through 255
      removed outlier: 4.126A  pdb=" N   ARG A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ALA A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   MET A 229 " --> pdb=" O   ARG A 225 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLY A 230 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ALA A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      Proline residue:  A 245  - end of helix
      removed outlier: 3.926A  pdb=" N   GLY A 255 " --> pdb=" O   TYR A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 278
      removed outlier: 4.246A  pdb=" N   PHE A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 297
    Processing helix  chain 'A' and resid 299 through 331
      removed outlier: 3.990A  pdb=" N   LEU A 319 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   GLU A 320 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
      Proline residue:  A 321  - end of helix
      Proline residue:  A 324  - end of helix
    Processing helix  chain 'A' and resid 336 through 342
      removed outlier: 4.209A  pdb=" N   LEU A 340 " --> pdb=" O   TRP A 336 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   PHE A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 364
      removed outlier: 5.086A  pdb=" N   ASN A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   LYS A 362 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
    Processing helix  chain 'A' and resid 384 through 386
      No H-bonds generated for 'chain 'A' and resid 384 through 386'
    Processing helix  chain 'A' and resid 389 through 391
      No H-bonds generated for 'chain 'A' and resid 389 through 391'
    Processing helix  chain 'A' and resid 392 through 422
      Proline residue:  A 412  - end of helix
      removed outlier: 4.145A  pdb=" N   GLY A 415 " --> pdb=" O   MET A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 455
      removed outlier: 3.677A  pdb=" N   TYR A 430 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLY A 444 " --> pdb=" O   GLY A 440 " (cutoff:3.500A)
      Proline residue:  A 445  - end of helix
      removed outlier: 5.337A  pdb=" N   GLY A 449 " --> pdb=" O   PRO A 445 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 472
    Processing helix  chain 'A' and resid 473 through 480
      removed outlier: 3.585A  pdb=" N   TYR A 477 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   SER A 480 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 54
      removed outlier: 4.071A  pdb=" N   LEU B  24 " --> pdb=" O   ARG B  20 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL B  25 " --> pdb=" O   GLN B  21 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   VAL B  42 " --> pdb=" O   PHE B  38 " (cutoff:3.500A)
      Proline residue:  B  43  - end of helix
      Proline residue:  B  46  - end of helix
      removed outlier: 3.689A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 154
      removed outlier: 4.443A  pdb=" N   THR B 137 " --> pdb=" O   GLU B 133 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ARG B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU B 142 " --> pdb=" O   ARG B 138 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE B 143 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   LYS B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   ALA B 147 " --> pdb=" O   PHE B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 165
      removed outlier: 3.947A  pdb=" N   LEU B 160 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASN B 162 " --> pdb=" O   GLY B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 187
      removed outlier: 3.541A  pdb=" N   MET B 170 " --> pdb=" O   TYR B 166 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA B 185 " --> pdb=" O   THR B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 219
      removed outlier: 3.690A  pdb=" N   LEU B 193 " --> pdb=" O   THR B 189 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL B 195 " --> pdb=" O   THR B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 250
      removed outlier: 4.128A  pdb=" N   ARG B 227 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ALA B 244 " --> pdb=" O   LEU B 240 " (cutoff:3.500A)
      Proline residue:  B 245  - end of helix
      removed outlier: 3.808A  pdb=" N   SER B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 276
      removed outlier: 3.547A  pdb=" N   LEU B 263 " --> pdb=" O   PRO B 259 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   CYS B 276 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
    Processing helix  chain 'B' and resid 299 through 318
      removed outlier: 4.212A  pdb=" N   GLY B 315 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   VAL B 316 " --> pdb=" O   ALA B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 331
      removed outlier: 4.208A  pdb=" N   THR B 322 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      Proline residue:  B 324  - end of helix
    Processing helix  chain 'B' and resid 339 through 341
      No H-bonds generated for 'chain 'B' and resid 339 through 341'
    Processing helix  chain 'B' and resid 342 through 364
      removed outlier: 3.619A  pdb=" N   SER B 346 " --> pdb=" O   PHE B 342 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TYR B 349 " --> pdb=" O   ALA B 345 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   ASN B 361 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   LYS B 362 " --> pdb=" O   VAL B 358 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   MET B 363 " --> pdb=" O   LEU B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 383
    Processing helix  chain 'B' and resid 384 through 386
      No H-bonds generated for 'chain 'B' and resid 384 through 386'
    Processing helix  chain 'B' and resid 388 through 391
    Processing helix  chain 'B' and resid 392 through 421
      Proline residue:  B 412  - end of helix
    Processing helix  chain 'B' and resid 427 through 455
      removed outlier: 3.522A  pdb=" N   ALA B 431 " --> pdb=" O   GLY B 427 " (cutoff:3.500A)
      Proline residue:  B 445  - end of helix
      removed outlier: 3.829A  pdb=" N   GLY B 449 " --> pdb=" O   PRO B 445 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ALA B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE B 451 " --> pdb=" O   THR B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 472
      removed outlier: 3.900A  pdb=" N   LEU B 460 " --> pdb=" O   GLY B 456 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   MET B 461 " --> pdb=" O   PHE B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 479

    445 hydrogen bonds defined for protein.
    1308 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: 1.55

  Time building geometry restraints manager: 1.85 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 861
        1.31 -     1.44: 1567
        1.44 -     1.56: 3386
        1.56 -     1.69: 2
        1.69 -     1.81: 100
  Bond restraints: 5916
  Sorted by residual:
  bond pdb=" C31 YHR B 601 "
       pdb=" O30 YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.326  1.402 -0.076 2.00e-02 2.50e+03 1.43e+01
  bond pdb=" C17 YHR B 601 "
       pdb=" O19 YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.325  1.396 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" CG  HSM A 601 "
       pdb=" ND1 HSM A 601 "
    ideal  model  delta    sigma   weight residual
    1.383  1.314  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" CD2 HSM A 601 "
       pdb=" NE2 HSM A 601 "
    ideal  model  delta    sigma   weight residual
    1.376  1.313  0.063 2.00e-02 2.50e+03 1.00e+01
  bond pdb=" N   ILE B 136 "
       pdb=" CA  ILE B 136 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.88e+00
  ... (remaining 5911 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.16: 8007
        4.16 -     8.32: 45
        8.32 -    12.49: 4
       12.49 -    16.65: 1
       16.65 -    20.81: 1
  Bond angle restraints: 8058
  Sorted by residual:
  angle pdb=" N   PHE B 131 "
        pdb=" CA  PHE B 131 "
        pdb=" C   PHE B 131 "
      ideal   model   delta    sigma   weight residual
     112.92   99.68   13.24 1.23e+00 6.61e-01 1.16e+02
  angle pdb=" C7  YHR B 601 "
        pdb=" N8  YHR B 601 "
        pdb=" C9  YHR B 601 "
      ideal   model   delta    sigma   weight residual
     111.89  132.70  -20.81 3.00e+00 1.11e-01 4.81e+01
  angle pdb=" N   GLY B 243 "
        pdb=" CA  GLY B 243 "
        pdb=" C   GLY B 243 "
      ideal   model   delta    sigma   weight residual
     112.50  118.55   -6.05 1.16e+00 7.43e-01 2.72e+01
  angle pdb=" N   PRO B 482 "
        pdb=" CA  PRO B 482 "
        pdb=" CB  PRO B 482 "
      ideal   model   delta    sigma   weight residual
     103.25   97.80    5.45 1.05e+00 9.07e-01 2.69e+01
  angle pdb=" C   GLN B  21 "
        pdb=" N   LEU B  22 "
        pdb=" CA  LEU B  22 "
      ideal   model   delta    sigma   weight residual
     121.54  130.23   -8.69 1.91e+00 2.74e-01 2.07e+01
  ... (remaining 8053 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.33: 3104
       23.33 -    46.65: 326
       46.65 -    69.97: 40
       69.97 -    93.30: 2
       93.30 -   116.62: 3
  Dihedral angle restraints: 3475
    sinusoidal: 1320
      harmonic: 2155
  Sorted by residual:
  dihedral pdb=" CA  PRO A  43 "
           pdb=" C   PRO A  43 "
           pdb=" N   ILE A  44 "
           pdb=" CA  ILE A  44 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.98  -21.02     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" C13 YHR B 601 "
           pdb=" C7  YHR B 601 "
           pdb=" N8  YHR B 601 "
           pdb=" C6  YHR B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.66  -58.96  116.62     1      3.00e+01 1.11e-03 1.54e+01
  dihedral pdb=" C   PRO B 482 "
           pdb=" N   PRO B 482 "
           pdb=" CA  PRO B 482 "
           pdb=" CB  PRO B 482 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -111.15   -9.55     0      2.50e+00 1.60e-01 1.46e+01
  ... (remaining 3472 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 873
       0.076 -    0.152: 88
       0.152 -    0.228: 5
       0.228 -    0.305: 1
       0.305 -    0.381: 1
  Chirality restraints: 968
  Sorted by residual:
  chirality pdb=" C13 YHR B 601 "
            pdb=" C12 YHR B 601 "
            pdb=" C14 YHR B 601 "
            pdb=" N8  YHR B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.67    0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" CA  PHE B 131 "
            pdb=" N   PHE B 131 "
            pdb=" C   PHE B 131 "
            pdb=" CB  PHE B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" C3  YHR B 601 "
            pdb=" C16 YHR B 601 "
            pdb=" C4  YHR B 601 "
            pdb=" O2  YHR B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.37    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 965 not shown)

  Planarity restraints: 982
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 472 "    0.090 5.00e-02 4.00e+02   1.34e-01 2.88e+01
        pdb=" N   PRO A 473 "   -0.232 5.00e-02 4.00e+02
        pdb=" CA  PRO A 473 "    0.072 5.00e-02 4.00e+02
        pdb=" CD  PRO A 473 "    0.070 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  20 "   -0.018 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   ARG B  20 "    0.062 2.00e-02 2.50e+03
        pdb=" O   ARG B  20 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLN B  21 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  42 "   -0.046 5.00e-02 4.00e+02   6.97e-02 7.77e+00
        pdb=" N   PRO B  43 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO B  43 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B  43 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 979 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 571
        2.74 -     3.28: 5993
        3.28 -     3.82: 9617
        3.82 -     4.36: 10439
        4.36 -     4.90: 18960
  Nonbonded interactions: 45580
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 442 "
            pdb=" OG  SER B 446 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   GLY B 140 "
            pdb=" N   PHE B 143 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" O   SER A 424 "
            pdb=" OG  SER A 424 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG  SER A 333 "
            pdb=" OE1 GLN A 337 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   GLN B  21 "
            pdb=" N   LEU B  24 "
     model   vdw
     2.303 3.120
  ... (remaining 45575 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 19 through 278 or resid 288 through 483))
  selection = (chain 'B' and (resid 19 through 51 or resid 135 through 483))
}

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 group one per residue
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:             2.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.820
  Find NCS groups from input model:        0.260
  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:             0.010
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
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      :  0.005   0.076   5916  Z= 0.286
  Angle     :  0.870  20.810   8058  Z= 0.488
  Chirality :  0.047   0.381    968
  Planarity :  0.009   0.134    982
  Dihedral  : 17.763 116.624   2105
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 20.27
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  1.72 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 34.47 %
    Favored  : 64.72 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.29), residues: 756
  helix:  1.03 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -1.29 (0.44), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 326 
 HIS   0.003   0.001   HIS B 416 
 PHE   0.039   0.002   PHE B  48 
 TYR   0.009   0.001   TYR A 251 
 ARG   0.005   0.001   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18189 (  445)
  hydrogen bonds       : angle       5.75747 ( 1308)
  covalent geometry    : bond        0.00534 ( 5916)
  covalent geometry    : angle       0.87021 ( 8058)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A  160 LEU cc_start: 0.8559 (tp) cc_final: 0.8290 (tt)
REVERT: A  414 MET cc_start: 0.7811 (mmm) cc_final: 0.7286 (mmm)
REVERT: B  132 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6711 (mm)
REVERT: B  135 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6711 (mp0)
REVERT: B  250 MET cc_start: 0.7854 (ttp) cc_final: 0.6951 (ppp)
REVERT: B  291 THR cc_start: 0.8024 (m) cc_final: 0.7745 (p)
REVERT: B  355 LEU cc_start: 0.7929 (tp) cc_final: 0.7649 (tt)
  outliers start: 5
  outliers final: 2
  residues processed: 137
  average time/residue: 0.1476
  time to fit residues: 27.9551
Evaluate side-chains
  129 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  482 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0010
   chunk 31 optimal weight:    0.2980
   chunk 19 optimal weight:    0.0970
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 59 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    0.4980
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.117311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.103748 restraints weight = 8938.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.106488 restraints weight = 4764.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.108301 restraints weight = 2998.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5916  Z= 0.153
  Angle     :  0.674   7.898   8058  Z= 0.337
  Chirality :  0.043   0.139    968
  Planarity :  0.005   0.041    982
  Dihedral  :  7.704  58.490    882
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 29.27 %
    Favored  : 66.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.31), residues: 756
  helix:  1.67 (0.22), residues: 596
  sheet:  None (None), residues: 0
  loop : -1.63 (0.45), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 326 
 HIS   0.002   0.001   HIS A 167 
 PHE   0.025   0.001   PHE A 356 
 TYR   0.011   0.001   TYR A 476 
 ARG   0.002   0.000   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05536 (  445)
  hydrogen bonds       : angle       4.45586 ( 1308)
  covalent geometry    : bond        0.00336 ( 5916)
  covalent geometry    : angle       0.67369 ( 8058)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A  153 VAL cc_start: 0.8245 (t) cc_final: 0.8031 (t)
REVERT: A  157 VAL cc_start: 0.8552 (t) cc_final: 0.8322 (p)
REVERT: A  212 LEU cc_start: 0.6410 (mt) cc_final: 0.6140 (mp)
REVERT: A  250 MET cc_start: 0.7389 (mmm) cc_final: 0.7167 (mmm)
REVERT: B  153 VAL cc_start: 0.8385 (t) cc_final: 0.8167 (p)
REVERT: B  355 LEU cc_start: 0.7809 (tp) cc_final: 0.7496 (tt)
REVERT: B  405 MET cc_start: 0.6908 (ttp) cc_final: 0.6668 (ttp)
REVERT: B  439 MET cc_start: 0.7396 (mmm) cc_final: 0.7110 (mmm)
  outliers start: 26
  outliers final: 13
  residues processed: 149
  average time/residue: 0.2185
  time to fit residues: 46.0764
Evaluate side-chains
  149 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 56 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 468 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.110717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.096220 restraints weight = 9047.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.099165 restraints weight = 4594.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.101118 restraints weight = 2801.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   5916  Z= 0.240
  Angle     :  0.709   7.980   8058  Z= 0.358
  Chirality :  0.047   0.188    968
  Planarity :  0.005   0.041    982
  Dihedral  :  6.557  49.602    874
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 27.97 %
    Favored  : 66.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.31), residues: 756
  helix:  1.62 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.14 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 336 
 HIS   0.004   0.001   HIS B 422 
 PHE   0.028   0.002   PHE A 356 
 TYR   0.016   0.002   TYR A 476 
 ARG   0.003   0.000   ARG A 421 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06825 (  445)
  hydrogen bonds       : angle       4.45017 ( 1308)
  covalent geometry    : bond        0.00570 ( 5916)
  covalent geometry    : angle       0.70888 ( 8058)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 0.576 
Fit side-chains
REVERT: A   41 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8216 (p)
REVERT: A  153 VAL cc_start: 0.8298 (t) cc_final: 0.8098 (t)
REVERT: A  246 PHE cc_start: 0.7664 (t80) cc_final: 0.7435 (t80)
REVERT: B  131 PHE cc_start: 0.6754 (p90) cc_final: 0.5766 (p90)
REVERT: B  135 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6229 (mp0)
REVERT: B  355 LEU cc_start: 0.7782 (tp) cc_final: 0.7533 (tt)
REVERT: B  409 SER cc_start: 0.7969 (m) cc_final: 0.7694 (p)
REVERT: B  417 LEU cc_start: 0.8004 (mt) cc_final: 0.7573 (mp)
REVERT: B  439 MET cc_start: 0.7442 (mmm) cc_final: 0.7216 (mmm)
  outliers start: 35
  outliers final: 19
  residues processed: 159
  average time/residue: 0.2001
  time to fit residues: 44.8520
Evaluate side-chains
  157 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  413 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** 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 = 0.3355 r_free = 0.3355 target = 0.111218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.096034 restraints weight = 9181.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.099169 restraints weight = 4570.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.101165 restraints weight = 2730.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   5916  Z= 0.197
  Angle     :  0.688   7.573   8058  Z= 0.344
  Chirality :  0.045   0.172    968
  Planarity :  0.005   0.045    982
  Dihedral  :  5.823  48.398    874
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 26.99 %
    Favored  : 66.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.32), residues: 756
  helix:  1.70 (0.22), residues: 601
  sheet:  None (None), residues: 0
  loop : -2.10 (0.47), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.003   0.001   HIS B 422 
 PHE   0.026   0.002   PHE A  38 
 TYR   0.013   0.002   TYR A 251 
 ARG   0.004   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06053 (  445)
  hydrogen bonds       : angle       4.33059 ( 1308)
  covalent geometry    : bond        0.00462 ( 5916)
  covalent geometry    : angle       0.68808 ( 8058)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 138
  time to evaluate  : 0.593 
Fit side-chains
REVERT: A   41 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8218 (p)
REVERT: A  229 MET cc_start: 0.7120 (mmm) cc_final: 0.6795 (mmm)
REVERT: A  313 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.6988 (m110)
REVERT: A  425 VAL cc_start: 0.7906 (t) cc_final: 0.7588 (m)
REVERT: B  135 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6583 (mp0)
REVERT: B  250 MET cc_start: 0.7147 (ttp) cc_final: 0.6723 (tmm)
REVERT: B  296 LEU cc_start: 0.7789 (tp) cc_final: 0.7564 (tt)
REVERT: B  316 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7632 (m)
REVERT: B  355 LEU cc_start: 0.7773 (tp) cc_final: 0.7516 (tt)
REVERT: B  363 MET cc_start: 0.7483 (ptm) cc_final: 0.7203 (ptt)
REVERT: B  411 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7260 (mpp)
REVERT: B  417 LEU cc_start: 0.8021 (mt) cc_final: 0.7623 (mp)
REVERT: B  439 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.7177 (mmm)
  outliers start: 38
  outliers final: 19
  residues processed: 160
  average time/residue: 0.1371
  time to fit residues: 30.3500
Evaluate side-chains
  160 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  313 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  411 MET
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  439 MET
Chi-restraints excluded: chain B residue  480 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 64 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** 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 = 0.3363 r_free = 0.3363 target = 0.112429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.097109 restraints weight = 9029.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.100195 restraints weight = 4522.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.102165 restraints weight = 2725.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5916  Z= 0.181
  Angle     :  0.665   7.221   8058  Z= 0.333
  Chirality :  0.044   0.153    968
  Planarity :  0.005   0.046    982
  Dihedral  :  5.584  49.020    874
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 28.62 %
    Favored  : 66.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.32), residues: 756
  helix:  1.77 (0.22), residues: 601
  sheet:  None (None), residues: 0
  loop : -2.14 (0.47), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.003   0.001   HIS B 422 
 PHE   0.024   0.001   PHE A  38 
 TYR   0.012   0.002   TYR A 476 
 ARG   0.007   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05824 (  445)
  hydrogen bonds       : angle       4.25882 ( 1308)
  covalent geometry    : bond        0.00419 ( 5916)
  covalent geometry    : angle       0.66539 ( 8058)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A   41 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8209 (p)
REVERT: A  229 MET cc_start: 0.7197 (mmm) cc_final: 0.6872 (mmm)
REVERT: A  254 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7740 (p)
REVERT: A  313 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.6983 (m-40)
REVERT: A  411 MET cc_start: 0.8281 (mmt) cc_final: 0.8052 (mmp)
REVERT: B  135 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6427 (mp0)
REVERT: B  153 VAL cc_start: 0.8382 (t) cc_final: 0.8156 (p)
REVERT: B  250 MET cc_start: 0.7215 (ttp) cc_final: 0.6722 (tmm)
REVERT: B  296 LEU cc_start: 0.7776 (tp) cc_final: 0.7556 (tt)
REVERT: B  355 LEU cc_start: 0.7746 (tp) cc_final: 0.7507 (tt)
REVERT: B  363 MET cc_start: 0.7452 (ptm) cc_final: 0.7185 (ptt)
REVERT: B  410 MET cc_start: 0.7911 (tpp) cc_final: 0.7339 (tpp)
REVERT: B  411 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7305 (mpp)
REVERT: B  417 LEU cc_start: 0.8031 (mt) cc_final: 0.7636 (mp)
REVERT: B  439 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7201 (mmm)
  outliers start: 33
  outliers final: 20
  residues processed: 157
  average time/residue: 0.1741
  time to fit residues: 37.8123
Evaluate side-chains
  163 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  313 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  443 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  411 MET
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  439 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 ASN ** 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 = 0.3330 r_free = 0.3330 target = 0.109437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.094390 restraints weight = 9068.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.097391 restraints weight = 4547.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.099341 restraints weight = 2742.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   5916  Z= 0.239
  Angle     :  0.704   7.405   8058  Z= 0.355
  Chirality :  0.047   0.191    968
  Planarity :  0.005   0.048    982
  Dihedral  :  5.592  47.947    874
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 28.13 %
    Favored  : 66.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.32), residues: 756
  helix:  1.60 (0.22), residues: 607
  sheet:  None (None), residues: 0
  loop : -2.00 (0.50), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 336 
 HIS   0.004   0.001   HIS B 422 
 PHE   0.024   0.002   PHE A  38 
 TYR   0.014   0.002   TYR A 349 
 ARG   0.007   0.001   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06597 (  445)
  hydrogen bonds       : angle       4.37979 ( 1308)
  covalent geometry    : bond        0.00564 ( 5916)
  covalent geometry    : angle       0.70430 ( 8058)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7513 (tpp) cc_final: 0.7299 (tpp)
REVERT: A   41 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8258 (p)
REVERT: A  229 MET cc_start: 0.7270 (mmm) cc_final: 0.6920 (mmm)
REVERT: A  254 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7793 (p)
REVERT: A  313 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7049 (m110)
REVERT: A  425 VAL cc_start: 0.7925 (t) cc_final: 0.7626 (m)
REVERT: B  135 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6447 (mp0)
REVERT: B  153 VAL cc_start: 0.8362 (t) cc_final: 0.8133 (p)
REVERT: B  250 MET cc_start: 0.7304 (ttp) cc_final: 0.7096 (ttp)
REVERT: B  296 LEU cc_start: 0.7777 (tp) cc_final: 0.7541 (tt)
REVERT: B  316 VAL cc_start: 0.7999 (OUTLIER) cc_final: 0.7680 (m)
REVERT: B  355 LEU cc_start: 0.7756 (tp) cc_final: 0.7527 (tt)
REVERT: B  363 MET cc_start: 0.7495 (ptm) cc_final: 0.7203 (ptt)
REVERT: B  411 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7242 (mpp)
REVERT: B  417 LEU cc_start: 0.7994 (mt) cc_final: 0.7628 (mp)
REVERT: B  439 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7234 (mmm)
  outliers start: 33
  outliers final: 18
  residues processed: 157
  average time/residue: 0.1663
  time to fit residues: 35.8756
Evaluate side-chains
  159 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  313 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  411 MET
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  439 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.110564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.095260 restraints weight = 9089.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.098298 restraints weight = 4559.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.100280 restraints weight = 2755.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   5916  Z= 0.206
  Angle     :  0.693   8.058   8058  Z= 0.347
  Chirality :  0.046   0.168    968
  Planarity :  0.005   0.049    982
  Dihedral  :  5.533  47.832    874
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 29.11 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.32), residues: 756
  helix:  1.66 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -2.05 (0.49), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 336 
 HIS   0.003   0.001   HIS B 422 
 PHE   0.021   0.001   PHE A  38 
 TYR   0.013   0.002   TYR A 349 
 ARG   0.005   0.001   ARG A 421 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06204 (  445)
  hydrogen bonds       : angle       4.34512 ( 1308)
  covalent geometry    : bond        0.00484 ( 5916)
  covalent geometry    : angle       0.69283 ( 8058)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A   41 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8221 (p)
REVERT: A  160 LEU cc_start: 0.8625 (tp) cc_final: 0.8362 (tt)
REVERT: A  229 MET cc_start: 0.7245 (mmm) cc_final: 0.6902 (mmm)
REVERT: A  313 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.7019 (m110)
REVERT: A  414 MET cc_start: 0.7486 (mmm) cc_final: 0.7030 (mmm)
REVERT: A  425 VAL cc_start: 0.7952 (t) cc_final: 0.7657 (m)
REVERT: B  135 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6443 (mp0)
REVERT: B  149 MET cc_start: 0.7826 (mmm) cc_final: 0.6977 (tpp)
REVERT: B  153 VAL cc_start: 0.8359 (t) cc_final: 0.8156 (p)
REVERT: B  296 LEU cc_start: 0.7784 (tp) cc_final: 0.7552 (tt)
REVERT: B  316 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7685 (m)
REVERT: B  355 LEU cc_start: 0.7767 (tp) cc_final: 0.7528 (tt)
REVERT: B  363 MET cc_start: 0.7463 (ptm) cc_final: 0.7191 (ptt)
REVERT: B  410 MET cc_start: 0.7800 (tpp) cc_final: 0.7150 (tpp)
REVERT: B  411 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7315 (mpp)
REVERT: B  417 LEU cc_start: 0.8026 (mt) cc_final: 0.7646 (mp)
  outliers start: 31
  outliers final: 21
  residues processed: 151
  average time/residue: 0.1481
  time to fit residues: 30.6842
Evaluate side-chains
  160 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  313 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  411 MET
Chi-restraints excluded: chain B residue  413 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 52 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 36 optimal weight:    0.4980
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.1980
   chunk 24 optimal weight:    0.1980
   overall best weight:    0.4180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.113416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.099144 restraints weight = 8719.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.101752 restraints weight = 4732.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.103555 restraints weight = 3032.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5916  Z= 0.157
  Angle     :  0.659   8.581   8058  Z= 0.329
  Chirality :  0.043   0.131    968
  Planarity :  0.006   0.065    982
  Dihedral  :  5.450  47.927    874
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 29.11 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.32), residues: 756
  helix:  1.88 (0.22), residues: 596
  sheet:  None (None), residues: 0
  loop : -2.14 (0.46), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 336 
 HIS   0.002   0.000   HIS B 422 
 PHE   0.019   0.001   PHE A  38 
 TYR   0.010   0.001   TYR A 476 
 ARG   0.005   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05317 (  445)
  hydrogen bonds       : angle       4.18404 ( 1308)
  covalent geometry    : bond        0.00356 ( 5916)
  covalent geometry    : angle       0.65856 ( 8058)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A   41 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8228 (p)
REVERT: A  160 LEU cc_start: 0.8656 (tp) cc_final: 0.8400 (tt)
REVERT: A  229 MET cc_start: 0.7204 (mmm) cc_final: 0.6889 (mmm)
REVERT: A  254 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7779 (p)
REVERT: A  411 MET cc_start: 0.8279 (mmt) cc_final: 0.8045 (mmp)
REVERT: A  414 MET cc_start: 0.7440 (mmm) cc_final: 0.6978 (mmm)
REVERT: B  135 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6424 (mp0)
REVERT: B  149 MET cc_start: 0.7700 (mmm) cc_final: 0.7223 (tpp)
REVERT: B  250 MET cc_start: 0.7097 (ttp) cc_final: 0.6875 (tmm)
REVERT: B  296 LEU cc_start: 0.7776 (tp) cc_final: 0.7562 (tt)
REVERT: B  355 LEU cc_start: 0.7794 (tp) cc_final: 0.7540 (tt)
REVERT: B  363 MET cc_start: 0.7329 (ptm) cc_final: 0.7085 (ptt)
REVERT: B  410 MET cc_start: 0.7814 (tpp) cc_final: 0.7183 (tpp)
REVERT: B  411 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7212 (mpp)
REVERT: B  417 LEU cc_start: 0.8090 (mt) cc_final: 0.7682 (mp)
  outliers start: 29
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1820
  time to fit residues: 38.3257
Evaluate side-chains
  161 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  411 MET
Chi-restraints excluded: chain B residue  413 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 22 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 37 optimal weight:    0.4980
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0980
   chunk 63 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.4180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.096597 restraints weight = 8871.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.099111 restraints weight = 4904.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.100789 restraints weight = 3166.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5916  Z= 0.156
  Angle     :  0.656   8.967   8058  Z= 0.327
  Chirality :  0.043   0.129    968
  Planarity :  0.005   0.054    982
  Dihedral  :  5.402  47.092    874
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 29.27 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.32), residues: 756
  helix:  1.88 (0.22), residues: 599
  sheet:  None (None), residues: 0
  loop : -2.06 (0.48), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.002   0.001   HIS A 167 
 PHE   0.018   0.001   PHE A  38 
 TYR   0.019   0.002   TYR A 477 
 ARG   0.005   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05303 (  445)
  hydrogen bonds       : angle       4.17580 ( 1308)
  covalent geometry    : bond        0.00353 ( 5916)
  covalent geometry    : angle       0.65551 ( 8058)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A   41 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8255 (p)
REVERT: A  160 LEU cc_start: 0.8639 (tp) cc_final: 0.8382 (tt)
REVERT: A  229 MET cc_start: 0.7220 (mmm) cc_final: 0.6917 (mmm)
REVERT: A  254 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7806 (p)
REVERT: A  313 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.6800 (m-40)
REVERT: A  411 MET cc_start: 0.8249 (mmt) cc_final: 0.8022 (mmp)
REVERT: A  414 MET cc_start: 0.7402 (mmm) cc_final: 0.6983 (mmm)
REVERT: B   36 MET cc_start: 0.7609 (ttt) cc_final: 0.7283 (ttt)
REVERT: B  135 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6443 (mp0)
REVERT: B  149 MET cc_start: 0.7583 (mmm) cc_final: 0.7193 (tpp)
REVERT: B  316 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7743 (m)
REVERT: B  355 LEU cc_start: 0.7821 (tp) cc_final: 0.7572 (tt)
REVERT: B  363 MET cc_start: 0.7254 (ptm) cc_final: 0.7029 (ptt)
REVERT: B  410 MET cc_start: 0.7782 (tpp) cc_final: 0.7182 (tpp)
REVERT: B  411 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7243 (mpp)
REVERT: B  417 LEU cc_start: 0.8115 (mt) cc_final: 0.7707 (mp)
  outliers start: 25
  outliers final: 18
  residues processed: 146
  average time/residue: 0.1458
  time to fit residues: 29.2798
Evaluate side-chains
  159 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  313 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  411 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.106795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.092956 restraints weight = 8907.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.095420 restraints weight = 4949.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.097098 restraints weight = 3210.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   5916  Z= 0.210
  Angle     :  0.703   8.889   8058  Z= 0.353
  Chirality :  0.046   0.171    968
  Planarity :  0.006   0.064    982
  Dihedral  :  5.475  46.916    874
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 28.62 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.32), residues: 756
  helix:  1.72 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.02 (0.49), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 422 
 PHE   0.027   0.002   PHE A 356 
 TYR   0.016   0.002   TYR A 477 
 ARG   0.004   0.000   ARG A 421 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06116 (  445)
  hydrogen bonds       : angle       4.25578 ( 1308)
  covalent geometry    : bond        0.00498 ( 5916)
  covalent geometry    : angle       0.70276 ( 8058)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.574 
Fit side-chains
REVERT: A   41 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8252 (p)
REVERT: A  160 LEU cc_start: 0.8642 (tp) cc_final: 0.8400 (tt)
REVERT: A  229 MET cc_start: 0.7258 (mmm) cc_final: 0.6931 (mmm)
REVERT: A  254 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7805 (p)
REVERT: A  297 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7723 (mt)
REVERT: A  313 ASN cc_start: 0.7546 (OUTLIER) cc_final: 0.6983 (m-40)
REVERT: A  411 MET cc_start: 0.8307 (mmt) cc_final: 0.8086 (mmp)
REVERT: A  425 VAL cc_start: 0.7898 (t) cc_final: 0.7594 (m)
REVERT: B  149 MET cc_start: 0.7748 (mmm) cc_final: 0.7295 (tpp)
REVERT: B  250 MET cc_start: 0.7174 (ttp) cc_final: 0.6832 (tmm)
REVERT: B  316 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7684 (m)
REVERT: B  355 LEU cc_start: 0.7721 (tp) cc_final: 0.7489 (tt)
REVERT: B  363 MET cc_start: 0.7405 (ptm) cc_final: 0.7138 (ptt)
REVERT: B  410 MET cc_start: 0.7860 (tpp) cc_final: 0.7223 (tpp)
REVERT: B  411 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7298 (mpp)
REVERT: B  417 LEU cc_start: 0.8037 (mt) cc_final: 0.7668 (mp)
  outliers start: 29
  outliers final: 20
  residues processed: 150
  average time/residue: 0.1383
  time to fit residues: 28.6015
Evaluate side-chains
  164 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  206 PHE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  313 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  170 MET
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  274 GLN
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  411 MET
Chi-restraints excluded: chain B residue  413 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0870
   chunk 65 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.108894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.095153 restraints weight = 8909.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.097630 restraints weight = 4904.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.099305 restraints weight = 3170.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5916  Z= 0.177
  Angle     :  0.684   9.104   8058  Z= 0.343
  Chirality :  0.044   0.148    968
  Planarity :  0.006   0.058    982
  Dihedral  :  5.161  45.539    871
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 29.59 %
    Favored  : 66.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.32), residues: 756
  helix:  1.80 (0.22), residues: 599
  sheet:  None (None), residues: 0
  loop : -2.05 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 336 
 HIS   0.002   0.001   HIS B 422 
 PHE   0.026   0.001   PHE A 356 
 TYR   0.016   0.002   TYR A 477 
 ARG   0.005   0.000   ARG A 421 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05687 (  445)
  hydrogen bonds       : angle       4.20043 ( 1308)
  covalent geometry    : bond        0.00410 ( 5916)
  covalent geometry    : angle       0.68391 ( 8058)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2312.16 seconds
wall clock time: 42 minutes 8.21 seconds (2528.21 seconds total)