Starting phenix.real_space_refine
on Fri Aug 22 16:23:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tgk_41239/08_2025/8tgk_41239_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tgk_41239/08_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_41239/08_2025/8tgk_41239.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tgk_41239/08_2025/8tgk_41239.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tgk_41239/08_2025/8tgk_41239_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tgk_41239/08_2025/8tgk_41239_trim.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.21, per 1000 atoms: 0.21
  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: 0.50
  Conformation dependent library (CDL) restraints added in 283.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.14
  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: 0.66

  Time building geometry restraints manager: 0.65 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:             2.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.270
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.300
-------------------------------------------------------------------------------
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 : 20.18
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.005   0.001   ARG A 227 
 TYR   0.009   0.001   TYR A 251 
 PHE   0.039   0.002   PHE B  48 
 TRP   0.014   0.002   TRP A 326 
 HIS   0.003   0.001   HIS B 416 

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

*********************** 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  : 0.132 
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: 0.0595
  time to fit residues: 11.3349
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  : 0.193 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.2980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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 = 0.3411 r_free = 0.3411 target = 0.113750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.100781 restraints weight = 9006.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.103353 restraints weight = 4919.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.105063 restraints weight = 3130.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.106201 restraints weight = 2257.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.106896 restraints weight = 1767.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5916  Z= 0.160
  Angle     :  0.681   8.143   8058  Z= 0.341
  Chirality :  0.044   0.130    968
  Planarity :  0.006   0.041    982
  Dihedral  :  7.626  59.201    882
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 29.27 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.31), residues: 756
  helix:  1.64 (0.22), residues: 596
  sheet:  None (None), residues: 0
  loop : -1.62 (0.46), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 227 
 TYR   0.012   0.001   TYR A 190 
 PHE   0.026   0.002   PHE A 356 
 TRP   0.009   0.001   TRP B 326 
 HIS   0.003   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 5916)
  covalent geometry    : angle       0.68086 ( 8058)
  hydrogen bonds       : bond        0.05658 (  445)
  hydrogen bonds       : angle       4.45215 ( 1308)

*********************** 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: 27
    poor density    : 134
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  153 VAL cc_start: 0.8369 (t) cc_final: 0.8161 (t)
REVERT: A  160 LEU cc_start: 0.8659 (tp) cc_final: 0.8363 (tt)
REVERT: A  212 LEU cc_start: 0.6561 (mt) cc_final: 0.6294 (mp)
REVERT: A  418 VAL cc_start: 0.8318 (p) cc_final: 0.8103 (t)
REVERT: B  153 VAL cc_start: 0.8456 (t) cc_final: 0.8250 (p)
REVERT: B  296 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7702 (tp)
REVERT: B  355 LEU cc_start: 0.7869 (tp) cc_final: 0.7544 (tt)
REVERT: B  405 MET cc_start: 0.6870 (ttp) cc_final: 0.6626 (ttp)
REVERT: B  439 MET cc_start: 0.7292 (mmm) cc_final: 0.7087 (mmm)
  outliers start: 27
  outliers final: 14
  residues processed: 149
  average time/residue: 0.0591
  time to fit residues: 12.4281
Evaluate side-chains
  150 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
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 A residue  423 THR
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  296 LEU
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 74 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 66 optimal weight:    0.3980
   chunk 30 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3372 r_free = 0.3372 target = 0.112710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.098024 restraints weight = 9059.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.101014 restraints weight = 4615.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.103006 restraints weight = 2811.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.104338 restraints weight = 1951.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.104932 restraints weight = 1486.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5916  Z= 0.185
  Angle     :  0.671   7.733   8058  Z= 0.335
  Chirality :  0.045   0.176    968
  Planarity :  0.005   0.042    982
  Dihedral  :  6.338  47.570    874
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 28.94 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.32), residues: 756
  helix:  1.74 (0.22), residues: 601
  sheet:  None (None), residues: 0
  loop : -2.04 (0.47), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 421 
 TYR   0.015   0.002   TYR A 251 
 PHE   0.027   0.001   PHE A 356 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 5916)
  covalent geometry    : angle       0.67119 ( 8058)
  hydrogen bonds       : bond        0.05978 (  445)
  hydrogen bonds       : angle       4.31777 ( 1308)

*********************** 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
  173 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 141
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   41 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8117 (p)
REVERT: A  160 LEU cc_start: 0.8699 (tp) cc_final: 0.8409 (tt)
REVERT: A  370 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7875 (tp)
REVERT: B  131 PHE cc_start: 0.6622 (p90) cc_final: 0.5714 (p90)
REVERT: B  135 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6231 (mp0)
REVERT: B  296 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7419 (mp)
REVERT: B  355 LEU cc_start: 0.7791 (tp) cc_final: 0.7511 (tt)
REVERT: B  405 MET cc_start: 0.6966 (ttp) cc_final: 0.6754 (ttm)
REVERT: B  409 SER cc_start: 0.7885 (m) cc_final: 0.7638 (p)
REVERT: B  417 LEU cc_start: 0.7976 (mt) cc_final: 0.7539 (mp)
REVERT: B  439 MET cc_start: 0.7381 (mmm) cc_final: 0.7145 (mmm)
  outliers start: 32
  outliers final: 17
  residues processed: 158
  average time/residue: 0.0524
  time to fit residues: 11.6458
Evaluate side-chains
  153 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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  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  370 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  135 GLU
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  154 ASN
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  389 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    0.0050
   chunk 73 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 58 optimal weight:    0.2980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.4394

-------------------------------------------------------------------------------
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 = 0.3360 r_free = 0.3360 target = 0.109740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.094946 restraints weight = 9067.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.097968 restraints weight = 4583.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.099949 restraints weight = 2779.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.101165 restraints weight = 1925.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.102090 restraints weight = 1492.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5916  Z= 0.160
  Angle     :  0.657   7.226   8058  Z= 0.327
  Chirality :  0.044   0.142    968
  Planarity :  0.005   0.043    982
  Dihedral  :  6.066  49.431    874
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 29.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.32), residues: 756
  helix:  1.82 (0.22), residues: 601
  sheet:  None (None), residues: 0
  loop : -2.07 (0.47), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 138 
 TYR   0.011   0.002   TYR A 251 
 PHE   0.027   0.001   PHE A  38 
 TRP   0.008   0.001   TRP A 336 
 HIS   0.003   0.001   HIS B 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5916)
  covalent geometry    : angle       0.65669 ( 8058)
  hydrogen bonds       : bond        0.05430 (  445)
  hydrogen bonds       : angle       4.22371 ( 1308)

*********************** 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
  164 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A   41 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8125 (p)
REVERT: A  160 LEU cc_start: 0.8686 (tp) cc_final: 0.8347 (tt)
REVERT: A  370 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7669 (tt)
REVERT: B  135 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6513 (mp0)
REVERT: B  250 MET cc_start: 0.7121 (ttp) cc_final: 0.6880 (tmm)
REVERT: B  355 LEU cc_start: 0.7801 (tp) cc_final: 0.7542 (tt)
REVERT: B  405 MET cc_start: 0.6981 (ttp) cc_final: 0.6773 (ttm)
REVERT: B  409 SER cc_start: 0.7912 (m) cc_final: 0.7655 (p)
REVERT: B  417 LEU cc_start: 0.7989 (mt) cc_final: 0.7552 (mp)
REVERT: B  439 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7147 (mmm)
  outliers start: 28
  outliers final: 16
  residues processed: 152
  average time/residue: 0.0558
  time to fit residues: 11.9673
Evaluate side-chains
  155 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  242 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  273 LEU
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  370 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  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  293 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  439 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3349 r_free = 0.3349 target = 0.111065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.095745 restraints weight = 9221.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.098824 restraints weight = 4654.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.100850 restraints weight = 2803.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.102195 restraints weight = 1939.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.103126 restraints weight = 1486.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   5916  Z= 0.211
  Angle     :  0.676   7.474   8058  Z= 0.339
  Chirality :  0.046   0.178    968
  Planarity :  0.005   0.044    982
  Dihedral  :  5.543  48.822    874
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 27.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.32), residues: 756
  helix:  1.74 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.15 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 138 
 TYR   0.016   0.002   TYR A 476 
 PHE   0.029   0.002   PHE A 356 
 TRP   0.010   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 5916)
  covalent geometry    : angle       0.67614 ( 8058)
  hydrogen bonds       : bond        0.06201 (  445)
  hydrogen bonds       : angle       4.28957 ( 1308)

*********************** 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
  172 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 133
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A   41 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8226 (p)
REVERT: A  254 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7703 (p)
REVERT: A  313 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.6936 (m110)
REVERT: B  135 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6397 (mp0)
REVERT: B  250 MET cc_start: 0.7217 (ttp) cc_final: 0.6820 (tmm)
REVERT: B  316 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7646 (m)
REVERT: B  405 MET cc_start: 0.6986 (ttp) cc_final: 0.6712 (ttm)
REVERT: B  410 MET cc_start: 0.7840 (tpp) cc_final: 0.7365 (tpp)
REVERT: B  411 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7232 (mpp)
REVERT: B  417 LEU cc_start: 0.7951 (mt) cc_final: 0.7541 (mp)
REVERT: B  439 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7211 (mmm)
  outliers start: 39
  outliers final: 19
  residues processed: 155
  average time/residue: 0.0520
  time to fit residues: 11.4617
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  : 0.137 
-------------------------------------------------------------------------------
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  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   21 GLN
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  154 ASN
Chi-restraints excluded: chain B residue  187 SER
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  439 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 37 optimal weight:    0.1980
   chunk 40 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0670
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 8 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.3118

-------------------------------------------------------------------------------
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 = 0.3392 r_free = 0.3392 target = 0.114139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.098610 restraints weight = 9057.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.101757 restraints weight = 4550.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.103862 restraints weight = 2743.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.105203 restraints weight = 1881.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.106128 restraints weight = 1442.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5916  Z= 0.141
  Angle     :  0.645   8.318   8058  Z= 0.317
  Chirality :  0.042   0.130    968
  Planarity :  0.005   0.044    982
  Dihedral  :  5.448  49.357    874
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 28.46 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.32), residues: 756
  helix:  1.97 (0.22), residues: 601
  sheet:  None (None), residues: 0
  loop : -2.02 (0.48), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 138 
 TYR   0.010   0.001   TYR A 476 
 PHE   0.024   0.001   PHE A 356 
 TRP   0.008   0.001   TRP A 336 
 HIS   0.002   0.000   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 5916)
  covalent geometry    : angle       0.64481 ( 8058)
  hydrogen bonds       : bond        0.05046 (  445)
  hydrogen bonds       : angle       4.14470 ( 1308)

*********************** 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
  168 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7441 (tpp) cc_final: 0.7187 (tpp)
REVERT: A   41 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8183 (p)
REVERT: A  160 LEU cc_start: 0.8672 (tp) cc_final: 0.8343 (tt)
REVERT: A  254 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7725 (p)
REVERT: A  313 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6681 (m-40)
REVERT: A  414 MET cc_start: 0.7494 (mmm) cc_final: 0.7006 (mmm)
REVERT: B  135 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6398 (mp0)
REVERT: B  296 LEU cc_start: 0.7741 (tp) cc_final: 0.7504 (tt)
REVERT: B  410 MET cc_start: 0.7908 (tpp) cc_final: 0.7662 (tpp)
REVERT: B  411 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7223 (mpp)
REVERT: B  439 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7170 (mmm)
  outliers start: 31
  outliers final: 16
  residues processed: 154
  average time/residue: 0.0540
  time to fit residues: 11.5978
Evaluate side-chains
  151 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
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  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  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   21 GLN
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  389 ILE
Chi-restraints excluded: chain B residue  411 MET
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 45 optimal weight:    0.1980
   chunk 47 optimal weight:    0.7980
   chunk 18 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 75 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.114647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.099489 restraints weight = 8999.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.102422 restraints weight = 4632.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.104418 restraints weight = 2866.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.105719 restraints weight = 2020.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.106595 restraints weight = 1579.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5916  Z= 0.157
  Angle     :  0.646   8.582   8058  Z= 0.320
  Chirality :  0.043   0.130    968
  Planarity :  0.005   0.061    982
  Dihedral  :  5.381  48.550    874
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 28.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.32), residues: 756
  helix:  1.95 (0.22), residues: 601
  sheet:  None (None), residues: 0
  loop : -1.96 (0.48), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 421 
 TYR   0.011   0.001   TYR A 476 
 PHE   0.023   0.001   PHE A 356 
 TRP   0.008   0.001   TRP A 336 
 HIS   0.002   0.000   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5916)
  covalent geometry    : angle       0.64649 ( 8058)
  hydrogen bonds       : bond        0.05265 (  445)
  hydrogen bonds       : angle       4.13618 ( 1308)

*********************** 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
  166 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7469 (tpp) cc_final: 0.7219 (tpp)
REVERT: A   41 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8191 (p)
REVERT: A  254 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7782 (p)
REVERT: A  313 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.6741 (m-40)
REVERT: A  410 MET cc_start: 0.7115 (mmp) cc_final: 0.6870 (mmp)
REVERT: A  414 MET cc_start: 0.7463 (mmm) cc_final: 0.6993 (mmm)
REVERT: B  135 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6457 (mp0)
REVERT: B  175 VAL cc_start: 0.7848 (t) cc_final: 0.7500 (p)
REVERT: B  296 LEU cc_start: 0.7698 (tp) cc_final: 0.7446 (tt)
REVERT: B  316 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7579 (m)
REVERT: B  410 MET cc_start: 0.7908 (tpp) cc_final: 0.7685 (mmm)
REVERT: B  411 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7194 (mpp)
REVERT: B  417 LEU cc_start: 0.8013 (mt) cc_final: 0.7583 (mp)
REVERT: B  439 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7191 (mmm)
  outliers start: 30
  outliers final: 18
  residues processed: 152
  average time/residue: 0.0571
  time to fit residues: 12.0600
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  : 0.202 
-------------------------------------------------------------------------------
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  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  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   21 GLN
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  439 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0980
   chunk 58 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0670
   overall best weight:    0.3718

-------------------------------------------------------------------------------
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  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.114865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.100495 restraints weight = 8861.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.103180 restraints weight = 4788.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.104908 restraints weight = 3069.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.106154 restraints weight = 2230.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.107022 restraints weight = 1752.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5916  Z= 0.148
  Angle     :  0.652   9.062   8058  Z= 0.321
  Chirality :  0.043   0.128    968
  Planarity :  0.005   0.056    982
  Dihedral  :  5.332  47.616    874
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 28.13 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.32), residues: 756
  helix:  1.99 (0.22), residues: 601
  sheet:  None (None), residues: 0
  loop : -1.90 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 138 
 TYR   0.010   0.001   TYR A 476 
 PHE   0.023   0.001   PHE A 356 
 TRP   0.008   0.001   TRP A 336 
 HIS   0.002   0.000   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 5916)
  covalent geometry    : angle       0.65190 ( 8058)
  hydrogen bonds       : bond        0.05118 (  445)
  hydrogen bonds       : angle       4.09464 ( 1308)

*********************** 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
  170 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 136
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7351 (tpp) cc_final: 0.7114 (tpp)
REVERT: A   41 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8248 (p)
REVERT: A  313 ASN cc_start: 0.7331 (OUTLIER) cc_final: 0.6737 (m110)
REVERT: B  135 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6434 (mp0)
REVERT: B  316 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7664 (m)
REVERT: B  410 MET cc_start: 0.7873 (tpp) cc_final: 0.7650 (mmm)
REVERT: B  411 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7239 (mpp)
REVERT: B  439 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7050 (mmm)
  outliers start: 34
  outliers final: 18
  residues processed: 153
  average time/residue: 0.0608
  time to fit residues: 13.0043
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  : 0.211 
-------------------------------------------------------------------------------
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  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  420 LEU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   21 GLN
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  439 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0970
   chunk 42 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 70 optimal weight:    0.2980
   chunk 39 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.110161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.096564 restraints weight = 8924.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.099049 restraints weight = 4923.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.100756 restraints weight = 3184.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.101818 restraints weight = 2314.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.102640 restraints weight = 1859.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5916  Z= 0.166
  Angle     :  0.676   9.710   8058  Z= 0.331
  Chirality :  0.043   0.128    968
  Planarity :  0.005   0.057    982
  Dihedral  :  5.343  46.875    874
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 28.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.32), residues: 756
  helix:  1.96 (0.22), residues: 601
  sheet:  None (None), residues: 0
  loop : -1.89 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 421 
 TYR   0.015   0.002   TYR A 477 
 PHE   0.025   0.001   PHE A 356 
 TRP   0.010   0.001   TRP A 336 
 HIS   0.002   0.001   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 5916)
  covalent geometry    : angle       0.67580 ( 8058)
  hydrogen bonds       : bond        0.05422 (  445)
  hydrogen bonds       : angle       4.11193 ( 1308)

*********************** 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
  164 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 137
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   36 MET cc_start: 0.7303 (tpp) cc_final: 0.7077 (tpp)
REVERT: A   41 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8295 (p)
REVERT: A  313 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.6851 (m110)
REVERT: B  135 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6427 (mp0)
REVERT: B  153 VAL cc_start: 0.8418 (t) cc_final: 0.8204 (p)
REVERT: B  316 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7710 (m)
REVERT: B  355 LEU cc_start: 0.7773 (tp) cc_final: 0.7530 (tt)
REVERT: B  410 MET cc_start: 0.7854 (tpp) cc_final: 0.7645 (mmm)
REVERT: B  411 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7257 (mpp)
REVERT: B  417 LEU cc_start: 0.8114 (mt) cc_final: 0.7683 (mp)
REVERT: B  439 MET cc_start: 0.7239 (mmm) cc_final: 0.7031 (mmm)
  outliers start: 27
  outliers final: 18
  residues processed: 152
  average time/residue: 0.0605
  time to fit residues: 12.8484
Evaluate side-chains
  159 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
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  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  420 LEU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   21 GLN
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 27 optimal weight:    0.3980
   chunk 64 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0980
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    0.2980
   chunk 22 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0470
   overall best weight:    0.3078

-------------------------------------------------------------------------------
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  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.116038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.100882 restraints weight = 8998.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.103883 restraints weight = 4698.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.105897 restraints weight = 2901.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.107252 restraints weight = 2031.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.108160 restraints weight = 1566.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5916  Z= 0.142
  Angle     :  0.660  10.719   8058  Z= 0.323
  Chirality :  0.042   0.138    968
  Planarity :  0.005   0.054    982
  Dihedral  :  5.337  46.989    874
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 28.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.32), residues: 756
  helix:  2.04 (0.22), residues: 601
  sheet:  None (None), residues: 0
  loop : -1.85 (0.48), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 421 
 TYR   0.010   0.001   TYR A 477 
 PHE   0.028   0.001   PHE B 356 
 TRP   0.008   0.001   TRP A 336 
 HIS   0.001   0.000   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 5916)
  covalent geometry    : angle       0.65979 ( 8058)
  hydrogen bonds       : bond        0.04973 (  445)
  hydrogen bonds       : angle       4.04112 ( 1308)

********************** 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
  163 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7426 (tpp) cc_final: 0.7221 (tpp)
REVERT: A   41 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8162 (p)
REVERT: A  313 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.6766 (m110)
REVERT: B  135 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6528 (mp0)
REVERT: B  153 VAL cc_start: 0.8243 (t) cc_final: 0.7993 (p)
REVERT: B  316 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7556 (m)
REVERT: B  410 MET cc_start: 0.7829 (tpp) cc_final: 0.7554 (tpp)
REVERT: B  411 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7186 (mpp)
REVERT: B  439 MET cc_start: 0.7391 (mmm) cc_final: 0.7073 (mmm)
  outliers start: 27
  outliers final: 18
  residues processed: 150
  average time/residue: 0.0612
  time to fit residues: 12.8590
Evaluate side-chains
  158 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
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  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  420 LEU
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   21 GLN
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 29 optimal weight:    0.1980
   chunk 12 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0010
   chunk 32 optimal weight:    0.0010
   chunk 40 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0570
   chunk 17 optimal weight:    0.3980
   chunk 64 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.1310

-------------------------------------------------------------------------------
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  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.117735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.103256 restraints weight = 8785.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.106012 restraints weight = 4764.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.107888 restraints weight = 3029.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.109097 restraints weight = 2180.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.109960 restraints weight = 1715.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5916  Z= 0.126
  Angle     :  0.657  10.600   8058  Z= 0.315
  Chirality :  0.041   0.124    968
  Planarity :  0.005   0.048    982
  Dihedral  :  5.260  47.032    874
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 29.27 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.32), residues: 756
  helix:  2.15 (0.22), residues: 598
  sheet:  None (None), residues: 0
  loop : -1.62 (0.50), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 138 
 TYR   0.008   0.001   TYR B 477 
 PHE   0.028   0.001   PHE A 356 
 TRP   0.007   0.001   TRP B 326 
 HIS   0.001   0.000   HIS B 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5916)
  covalent geometry    : angle       0.65670 ( 8058)
  hydrogen bonds       : bond        0.04296 (  445)
  hydrogen bonds       : angle       3.97156 ( 1308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 943.90 seconds
wall clock time: 16 minutes 57.61 seconds (1017.61 seconds total)