Starting phenix.real_space_refine
on Wed Mar 12 07:54:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j84_36059/03_2025/8j84_36059.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j84_36059/03_2025/8j84_36059.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j84_36059/03_2025/8j84_36059.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j84_36059/03_2025/8j84_36059.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j84_36059/03_2025/8j84_36059.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j84_36059/03_2025/8j84_36059.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.016
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      23      5.16       5
     C    4818      2.51       5
     N    1240      2.21       5
     O    1367      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7448
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3689
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 26, 'TRANS': 429}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 450, 3759
          Classifications: {'peptide': 450}
          Link IDs: {'PTRANS': 14, 'TRANS': 435}
  Time building chain proxies: 4.95, per 1000 atoms: 0.66
  Number of scatterers: 7448
  At special positions: 0
  Unit cell: (77.7, 84, 132.3, 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      23     16.00
     O    1367      8.00
     N    1240      7.00
     C    4818      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.92
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1724

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 12 sheets defined
      41.7% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 17
      No H-bonds generated for 'chain 'A' and resid 15 through 17'
    Processing helix  chain 'A' and resid 22 through 31
    Processing helix  chain 'A' and resid 46 through 62
      removed outlier: 3.776A  pdb=" N   GLN A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LYS A  62 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 82
    Processing helix  chain 'A' and resid 97 through 105
      removed outlier: 4.151A  pdb=" N   ILE A 101 " --> pdb=" O   THR A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 132
      removed outlier: 4.107A  pdb=" N   ASP A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 150
    Processing helix  chain 'A' and resid 205 through 217
      removed outlier: 4.416A  pdb=" N   GLN A 209 " --> pdb=" O   GLN A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 230
    Processing helix  chain 'A' and resid 231 through 234
    Processing helix  chain 'A' and resid 248 through 264
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'A' and resid 366 through 377
      removed outlier: 3.598A  pdb=" N   TRP A 370 " --> pdb=" O   ASN A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 464
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 3.788A  pdb=" N   PHE A 482 " --> pdb=" O   VAL A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 493
    Processing helix  chain 'B' and resid 14 through 29
      removed outlier: 4.033A  pdb=" N   THR B  18 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
      removed outlier: 3.541A  pdb=" N   LEU B  37 " --> pdb=" O   CYS B  34 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU B  39 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 56
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 4.257A  pdb=" N   LYS B  70 " --> pdb=" O   THR B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 88
    Processing helix  chain 'B' and resid 109 through 114
      removed outlier: 4.371A  pdb=" N   ARG B 114 " --> pdb=" O   ILE B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 138
    Processing helix  chain 'B' and resid 146 through 158
      removed outlier: 4.021A  pdb=" N   SER B 150 " --> pdb=" O   ASP B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 194
    Processing helix  chain 'B' and resid 199 through 203
    Processing helix  chain 'B' and resid 221 through 226
      removed outlier: 3.695A  pdb=" N   ILE B 224 " --> pdb=" O   TYR B 221 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   HIS B 225 " --> pdb=" O   ASP B 222 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLN B 226 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 221 through 226'
    Processing helix  chain 'B' and resid 243 through 249
    Processing helix  chain 'B' and resid 257 through 277
      removed outlier: 3.527A  pdb=" N   CYS B 261 " --> pdb=" O   ARG B 257 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLN B 262 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ARG B 263 " --> pdb=" O   TYR B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 280
      No H-bonds generated for 'chain 'B' and resid 278 through 280'
    Processing helix  chain 'B' and resid 300 through 304
    Processing helix  chain 'B' and resid 353 through 366
      removed outlier: 3.588A  pdb=" N   GLN B 357 " --> pdb=" O   SER B 353 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ARG B 362 " --> pdb=" O   HIS B 358 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   LYS B 363 " --> pdb=" O   SER B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 385
      removed outlier: 4.604A  pdb=" N   LYS B 376 " --> pdb=" O   LYS B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 424
      No H-bonds generated for 'chain 'B' and resid 422 through 424'
    Processing helix  chain 'B' and resid 425 through 434
      removed outlier: 3.683A  pdb=" N   ALA B 431 " --> pdb=" O   GLU B 427 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ASP B 432 " --> pdb=" O   SER B 428 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ASN B 434 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 448
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6
      removed outlier: 6.659A  pdb=" N   GLY A 385 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
      removed outlier: 5.400A  pdb=" N   VAL A 357 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   VAL A 386 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   ILE A 359 " --> pdb=" O   VAL A 386 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE A 388 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   ALA A 361 " --> pdb=" O   ILE A 388 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20
      removed outlier: 3.540A  pdb=" N   GLN A  18 " --> pdb=" O   PHE A  14 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 95
      removed outlier: 7.089A  pdb=" N   VAL A  43 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   GLY A  42 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   ILE A 142 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   VAL A  44 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 287
    Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 287
      removed outlier: 4.044A  pdb=" N   LEU A 501 " --> pdb=" O   VAL A 312 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398
    Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 426
      removed outlier: 3.826A  pdb=" N   SER A 431 " --> pdb=" O   VAL A 426 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 6
      removed outlier: 7.082A  pdb=" N   ILE B   5 " --> pdb=" O   TRP B  33 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 63
      removed outlier: 6.573A  pdb=" N   ILE B  62 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 283 through 286
      removed outlier: 6.203A  pdb=" N   PHE B 291 " --> pdb=" O   ALA B 325 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   ALA B 325 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 283 through 286
      removed outlier: 6.203A  pdb=" N   PHE B 291 " --> pdb=" O   ALA B 325 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   ALA B 325 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LEU B 402 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.944A  pdb=" N   ILE B 208 " --> pdb=" O   CYS B 215 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   CYS B 215 " --> pdb=" O   ILE B 208 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   TYR B 210 " --> pdb=" O   TYR B 213 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    864 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 2.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2361
        1.34 -     1.46: 1367
        1.46 -     1.57: 3869
        1.57 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 7632
  Sorted by residual:
  bond pdb=" CB  LYS A 290 "
       pdb=" CG  LYS A 290 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.07e+00
  bond pdb=" CA  PHE B  60 "
       pdb=" CB  PHE B  60 "
    ideal  model  delta    sigma   weight residual
    1.538  1.562 -0.024 2.12e-02 2.22e+03 1.30e+00
  bond pdb=" CA  THR A 218 "
       pdb=" CB  THR A 218 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.51e-02 4.39e+03 9.65e-01
  bond pdb=" CG  ARG A 103 "
       pdb=" CD  ARG A 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.32e-01
  bond pdb=" CB  GLU B 306 "
       pdb=" CG  GLU B 306 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.85e-01
  ... (remaining 7627 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 10152
        1.85 -     3.70: 122
        3.70 -     5.55: 25
        5.55 -     7.40: 9
        7.40 -     9.25: 4
  Bond angle restraints: 10312
  Sorted by residual:
  angle pdb=" N   VAL B  43 "
        pdb=" CA  VAL B  43 "
        pdb=" C   VAL B  43 "
      ideal   model   delta    sigma   weight residual
     111.62  107.05    4.57 7.90e-01 1.60e+00 3.35e+01
  angle pdb=" CB  LYS A 290 "
        pdb=" CG  LYS A 290 "
        pdb=" CD  LYS A 290 "
      ideal   model   delta    sigma   weight residual
     111.30  120.55   -9.25 2.30e+00 1.89e-01 1.62e+01
  angle pdb=" CA  LYS A 290 "
        pdb=" CB  LYS A 290 "
        pdb=" CG  LYS A 290 "
      ideal   model   delta    sigma   weight residual
     114.10  121.45   -7.35 2.00e+00 2.50e-01 1.35e+01
  angle pdb=" CA  GLU B 306 "
        pdb=" CB  GLU B 306 "
        pdb=" CG  GLU B 306 "
      ideal   model   delta    sigma   weight residual
     114.10  120.01   -5.91 2.00e+00 2.50e-01 8.72e+00
  angle pdb=" CA  LEU A 462 "
        pdb=" CB  LEU A 462 "
        pdb=" CG  LEU A 462 "
      ideal   model   delta    sigma   weight residual
     116.30  125.03   -8.73 3.50e+00 8.16e-02 6.21e+00
  ... (remaining 10307 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 3875
       17.70 -    35.39: 562
       35.39 -    53.09: 117
       53.09 -    70.79: 28
       70.79 -    88.49: 10
  Dihedral angle restraints: 4592
    sinusoidal: 1927
      harmonic: 2665
  Sorted by residual:
  dihedral pdb=" CA  LYS B 137 "
           pdb=" C   LYS B 137 "
           pdb=" N   GLN B 138 "
           pdb=" CA  GLN B 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.52   18.48     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ASP B 222 "
           pdb=" CB  ASP B 222 "
           pdb=" CG  ASP B 222 "
           pdb=" OD1 ASP B 222 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.68   58.68     1      2.00e+01 2.50e-03 1.15e+01
  dihedral pdb=" CA  MET A 406 "
           pdb=" C   MET A 406 "
           pdb=" N   ARG A 407 "
           pdb=" CA  ARG A 407 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.92   16.08     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 4589 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 693
       0.034 -    0.068: 283
       0.068 -    0.102: 83
       0.102 -    0.136: 45
       0.136 -    0.170: 2
  Chirality restraints: 1106
  Sorted by residual:
  chirality pdb=" CB  THR A 119 "
            pdb=" CA  THR A 119 "
            pdb=" OG1 THR A 119 "
            pdb=" CG2 THR A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.19e-01
  chirality pdb=" CB  THR A 463 "
            pdb=" CA  THR A 463 "
            pdb=" OG1 THR A 463 "
            pdb=" CG2 THR A 463 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 4.99e-01
  chirality pdb=" CG  LEU A 423 "
            pdb=" CB  LEU A 423 "
            pdb=" CD1 LEU A 423 "
            pdb=" CD2 LEU A 423 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.39e-01
  ... (remaining 1103 not shown)

  Planarity restraints: 1312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  60 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.94e+00
        pdb=" C   PHE B  60 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   PHE B  60 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU B  61 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  60 "    0.009 2.00e-02 2.50e+03   1.14e-02 2.26e+00
        pdb=" CG  PHE B  60 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  60 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  60 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  60 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  60 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  60 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 285 "    0.007 2.00e-02 2.50e+03   8.65e-03 1.50e+00
        pdb=" CG  TYR A 285 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 285 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 285 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 285 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 285 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 285 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 285 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1309 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 331
        2.71 -     3.26: 7812
        3.26 -     3.81: 12917
        3.81 -     4.35: 15474
        4.35 -     4.90: 25397
  Nonbonded interactions: 61931
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 269 "
            pdb=" OH  TYR A 467 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" NE2 GLN A 205 "
            pdb=" O   ASP B 439 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OG1 THR B  57 "
            pdb=" O   LYS B  59 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   SER A  88 "
            pdb=" OG  SER A  88 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" N   GLN A 295 "
            pdb=" OE1 GLN A 295 "
     model   vdw
     2.230 3.120
  ... (remaining 61926 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.080
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:3.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
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      :  0.002   0.043   7632  Z= 0.151
  Angle     :  0.581   9.248  10312  Z= 0.298
  Chirality :  0.043   0.170   1106
  Planarity :  0.003   0.032   1312
  Dihedral  : 17.270  88.487   2868
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 27.59 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.28), residues: 900
  helix:  0.61 (0.30), residues: 314
  sheet: -1.26 (0.42), residues: 139
  loop : -1.40 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 370 
 HIS   0.005   0.001   HIS B 358 
 PHE   0.024   0.001   PHE B  60 
 TYR   0.018   0.001   TYR A 285 
 ARG   0.007   0.000   ARG A 103 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 89
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 HIS cc_start: 0.8814 (m-70) cc_final: 0.8344 (t-170)
REVERT: A  295 GLN cc_start: 0.9062 (pm20) cc_final: 0.8649 (pm20)
REVERT: A  348 GLU cc_start: 0.9408 (pp20) cc_final: 0.9091 (pp20)
REVERT: A  474 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6491 (p0)
REVERT: B   75 LEU cc_start: 0.9178 (mm) cc_final: 0.8928 (mm)
REVERT: B  172 ASP cc_start: 0.8126 (t0) cc_final: 0.7822 (t0)
REVERT: B  345 MET cc_start: 0.8793 (mtm) cc_final: 0.8412 (mtm)
REVERT: B  348 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8624 (mp)
REVERT: B  369 TRP cc_start: 0.7515 (m-90) cc_final: 0.6825 (m-90)
REVERT: B  371 ASP cc_start: 0.8002 (p0) cc_final: 0.6950 (m-30)
REVERT: B  375 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6843 (mp0)
  outliers start: 35
  outliers final: 29
  residues processed: 116
  average time/residue: 0.1795
  time to fit residues: 29.0678
Evaluate side-chains
  119 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 87
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  148 TYR
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  474 ASP
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  160 HIS
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  229 LYS
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  354 LYS
Chi-restraints excluded: chain B residue  367 ASN
Chi-restraints excluded: chain B residue  375 GLU
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  438 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 68 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0970
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0040
   chunk 52 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.2194

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 205 GLN
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.104760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.082394 restraints weight = 18626.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 4.65
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7632  Z= 0.254
  Angle     :  0.574   6.804  10312  Z= 0.300
  Chirality :  0.044   0.174   1106
  Planarity :  0.003   0.031   1312
  Dihedral  :  8.388  59.321   1040
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 24.51 %
    Favored  : 69.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.28), residues: 900
  helix:  0.60 (0.30), residues: 318
  sheet: -1.47 (0.42), residues: 128
  loop : -1.50 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 369 
 HIS   0.006   0.001   HIS B 358 
 PHE   0.016   0.002   PHE B  60 
 TYR   0.012   0.001   TYR B 330 
 ARG   0.004   0.000   ARG A 102 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 96
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 ASP cc_start: 0.8354 (t0) cc_final: 0.8013 (t0)
REVERT: B  223 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.9017 (t80)
REVERT: B  345 MET cc_start: 0.8741 (mtm) cc_final: 0.8331 (mtm)
REVERT: B  371 ASP cc_start: 0.7945 (p0) cc_final: 0.7501 (m-30)
  outliers start: 49
  outliers final: 29
  residues processed: 131
  average time/residue: 0.1848
  time to fit residues: 33.4842
Evaluate side-chains
  117 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 87
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  148 TYR
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  160 HIS
Chi-restraints excluded: chain B residue  162 LYS
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  354 LYS
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   chunk 17 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.103754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.081108 restraints weight = 19027.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 4.71
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7632  Z= 0.251
  Angle     :  0.577   7.473  10312  Z= 0.299
  Chirality :  0.044   0.180   1106
  Planarity :  0.003   0.031   1312
  Dihedral  :  6.989  57.480   1005
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 23.52 %
    Favored  : 69.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.28), residues: 900
  helix:  0.52 (0.30), residues: 317
  sheet: -1.43 (0.43), residues: 128
  loop : -1.47 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 369 
 HIS   0.006   0.001   HIS B 358 
 PHE   0.018   0.002   PHE B  60 
 TYR   0.014   0.001   TYR B 330 
 ARG   0.006   0.000   ARG A 102 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 96
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 MET cc_start: 0.7709 (ttm) cc_final: 0.7301 (ttm)
REVERT: B   16 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.7998 (p0)
REVERT: B  172 ASP cc_start: 0.8337 (t0) cc_final: 0.7945 (t0)
REVERT: B  345 MET cc_start: 0.8736 (mtm) cc_final: 0.8318 (mtm)
REVERT: B  348 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8627 (mp)
REVERT: B  371 ASP cc_start: 0.7961 (p0) cc_final: 0.7559 (m-30)
REVERT: B  430 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8109 (mp)
  outliers start: 55
  outliers final: 37
  residues processed: 132
  average time/residue: 0.1804
  time to fit residues: 33.3279
Evaluate side-chains
  127 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 87
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   16 ASP
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  160 HIS
Chi-restraints excluded: chain B residue  162 LYS
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  354 LYS
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  430 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 88 optimal weight:    0.6980
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.101682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.079096 restraints weight = 19056.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 4.67
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   7632  Z= 0.309
  Angle     :  0.596   7.651  10312  Z= 0.311
  Chirality :  0.045   0.188   1106
  Planarity :  0.004   0.032   1312
  Dihedral  :  6.654  57.420    999
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  6.53 %
    Allowed  : 23.77 %
    Favored  : 69.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.27), residues: 900
  helix:  0.25 (0.29), residues: 325
  sheet: -1.55 (0.43), residues: 128
  loop : -1.48 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 369 
 HIS   0.006   0.001   HIS B 358 
 PHE   0.018   0.002   PHE B  60 
 TYR   0.019   0.001   TYR B 330 
 ARG   0.005   0.000   ARG A 103 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 88
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 HIS cc_start: 0.8773 (m-70) cc_final: 0.8253 (t-170)
REVERT: A  356 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6555 (mp0)
REVERT: B   16 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8003 (p0)
REVERT: B  138 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7976 (tm-30)
REVERT: B  172 ASP cc_start: 0.8383 (t0) cc_final: 0.7960 (t0)
REVERT: B  223 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8951 (t80)
REVERT: B  371 ASP cc_start: 0.7965 (p0) cc_final: 0.7738 (m-30)
REVERT: B  430 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8486 (mp)
  outliers start: 53
  outliers final: 41
  residues processed: 125
  average time/residue: 0.1774
  time to fit residues: 31.6127
Evaluate side-chains
  125 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 80
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   16 ASP
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  160 HIS
Chi-restraints excluded: chain B residue  162 LYS
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  223 PHE
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  354 LYS
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  430 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 41 optimal weight:    0.4980
   chunk 80 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.105208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.082607 restraints weight = 18649.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 4.68
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7632  Z= 0.179
  Angle     :  0.564   7.939  10312  Z= 0.287
  Chirality :  0.044   0.190   1106
  Planarity :  0.003   0.031   1312
  Dihedral  :  6.333  56.369    999
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 24.01 %
    Favored  : 69.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.27), residues: 900
  helix:  0.54 (0.30), residues: 317
  sheet: -1.19 (0.42), residues: 138
  loop : -1.55 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 231 
 HIS   0.005   0.001   HIS B 358 
 PHE   0.021   0.001   PHE B  60 
 TYR   0.013   0.001   TYR B 330 
 ARG   0.003   0.000   ARG A 102 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 95
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 HIS cc_start: 0.8741 (m-70) cc_final: 0.8248 (t-170)
REVERT: A  112 LYS cc_start: 0.9783 (tppt) cc_final: 0.9534 (tppt)
REVERT: A  356 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6662 (mm-30)
REVERT: A  362 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7744 (ptp-170)
REVERT: B   16 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8006 (p0)
REVERT: B  138 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7949 (tm-30)
REVERT: B  172 ASP cc_start: 0.8366 (t0) cc_final: 0.7862 (t0)
REVERT: B  345 MET cc_start: 0.8620 (mtt) cc_final: 0.8337 (ptt)
REVERT: B  371 ASP cc_start: 0.8044 (p0) cc_final: 0.7766 (m-30)
  outliers start: 51
  outliers final: 36
  residues processed: 133
  average time/residue: 0.1743
  time to fit residues: 32.3911
Evaluate side-chains
  124 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 85
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  362 ARG
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   16 ASP
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  160 HIS
Chi-restraints excluded: chain B residue  162 LYS
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  354 LYS
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  427 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 27 optimal weight:    0.4980
   chunk 14 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.104532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.082428 restraints weight = 18488.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 4.62
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7632  Z= 0.197
  Angle     :  0.562   8.087  10312  Z= 0.288
  Chirality :  0.045   0.199   1106
  Planarity :  0.003   0.031   1312
  Dihedral  :  6.244  55.865    998
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 25.74 %
    Favored  : 68.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.28), residues: 900
  helix:  0.45 (0.30), residues: 321
  sheet: -1.27 (0.43), residues: 128
  loop : -1.49 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 231 
 HIS   0.006   0.001   HIS B 358 
 PHE   0.022   0.001   PHE B  60 
 TYR   0.013   0.001   TYR B 330 
 ARG   0.003   0.000   ARG A 102 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 88
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 HIS cc_start: 0.8755 (m-70) cc_final: 0.8256 (t-170)
REVERT: A  112 LYS cc_start: 0.9793 (tppt) cc_final: 0.9532 (tppt)
REVERT: A  356 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6786 (mm-30)
REVERT: A  368 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8269 (pm20)
REVERT: B   16 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.7980 (p0)
REVERT: B  138 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7922 (tm-30)
REVERT: B  172 ASP cc_start: 0.8392 (t0) cc_final: 0.7924 (t0)
REVERT: B  274 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: B  345 MET cc_start: 0.8606 (mtt) cc_final: 0.8365 (ptt)
REVERT: B  371 ASP cc_start: 0.8079 (p0) cc_final: 0.7867 (m-30)
  outliers start: 48
  outliers final: 36
  residues processed: 124
  average time/residue: 0.1739
  time to fit residues: 30.1941
Evaluate side-chains
  123 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 84
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   16 ASP
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  160 HIS
Chi-restraints excluded: chain B residue  162 LYS
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  354 LYS
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  421 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 68 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0170
   chunk 22 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    1.1424

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.103590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.081480 restraints weight = 18605.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 4.60
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7632  Z= 0.243
  Angle     :  0.580   7.707  10312  Z= 0.299
  Chirality :  0.045   0.209   1106
  Planarity :  0.003   0.031   1312
  Dihedral  :  6.333  55.580    998
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 25.25 %
    Favored  : 68.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.28), residues: 900
  helix:  0.49 (0.30), residues: 316
  sheet: -1.34 (0.43), residues: 128
  loop : -1.44 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 369 
 HIS   0.004   0.001   HIS B 358 
 PHE   0.032   0.001   PHE B  60 
 TYR   0.017   0.001   TYR B 330 
 ARG   0.002   0.000   ARG A 362 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 84
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8265 (mmmt)
REVERT: A  111 HIS cc_start: 0.8770 (m-70) cc_final: 0.8315 (t-170)
REVERT: A  112 LYS cc_start: 0.9795 (tppt) cc_final: 0.9534 (tppt)
REVERT: A  356 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6931 (mp0)
REVERT: A  368 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8334 (pm20)
REVERT: B   16 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8020 (p0)
REVERT: B  138 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7969 (tm-30)
REVERT: B  172 ASP cc_start: 0.8367 (t0) cc_final: 0.7836 (t0)
REVERT: B  274 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7929 (tm-30)
REVERT: B  345 MET cc_start: 0.8622 (mtt) cc_final: 0.8347 (ptt)
REVERT: B  371 ASP cc_start: 0.8069 (p0) cc_final: 0.7825 (m-30)
  outliers start: 51
  outliers final: 45
  residues processed: 120
  average time/residue: 0.1810
  time to fit residues: 30.7485
Evaluate side-chains
  126 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 78
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   16 ASP
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  160 HIS
Chi-restraints excluded: chain B residue  162 LYS
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  354 LYS
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  421 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.104433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.082534 restraints weight = 18703.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 4.60
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7632  Z= 0.209
  Angle     :  0.563   7.443  10312  Z= 0.290
  Chirality :  0.045   0.211   1106
  Planarity :  0.003   0.031   1312
  Dihedral  :  6.260  54.894    998
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 25.49 %
    Favored  : 68.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.28), residues: 900
  helix:  0.52 (0.30), residues: 316
  sheet: -1.30 (0.43), residues: 128
  loop : -1.44 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 231 
 HIS   0.003   0.001   HIS B 358 
 PHE   0.034   0.001   PHE B  60 
 TYR   0.014   0.001   TYR A 285 
 ARG   0.002   0.000   ARG A 102 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 84
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8269 (mmmt)
REVERT: A  111 HIS cc_start: 0.8808 (m-70) cc_final: 0.8369 (t-170)
REVERT: A  112 LYS cc_start: 0.9795 (tppt) cc_final: 0.9538 (tppt)
REVERT: A  356 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6877 (mp0)
REVERT: A  368 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8326 (pm20)
REVERT: B   16 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.7928 (p0)
REVERT: B  138 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7969 (tm-30)
REVERT: B  172 ASP cc_start: 0.8354 (t0) cc_final: 0.7803 (t0)
REVERT: B  345 MET cc_start: 0.8598 (mtt) cc_final: 0.8325 (ptt)
REVERT: B  425 GLU cc_start: 0.9220 (pm20) cc_final: 0.8963 (pm20)
REVERT: B  426 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8269 (mp0)
  outliers start: 51
  outliers final: 43
  residues processed: 120
  average time/residue: 0.1766
  time to fit residues: 29.8914
Evaluate side-chains
  129 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 82
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   16 ASP
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  160 HIS
Chi-restraints excluded: chain B residue  162 LYS
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  354 LYS
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain B residue  426 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 85 optimal weight:    0.1980
   chunk 45 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 70 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.103659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.081560 restraints weight = 18970.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 4.65
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7632  Z= 0.249
  Angle     :  0.585   7.798  10312  Z= 0.302
  Chirality :  0.045   0.219   1106
  Planarity :  0.003   0.031   1312
  Dihedral  :  6.359  55.005    998
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 25.74 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.28), residues: 900
  helix:  0.46 (0.30), residues: 316
  sheet: -1.36 (0.43), residues: 128
  loop : -1.44 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 231 
 HIS   0.003   0.001   HIS B 358 
 PHE   0.030   0.001   PHE B  60 
 TYR   0.016   0.001   TYR A 285 
 ARG   0.002   0.000   ARG A 102 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 80
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8303 (mmmt)
REVERT: A  111 HIS cc_start: 0.8803 (m-70) cc_final: 0.8320 (t-170)
REVERT: A  112 LYS cc_start: 0.9796 (tppt) cc_final: 0.9538 (tppt)
REVERT: A  356 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6943 (mp0)
REVERT: A  368 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8341 (pm20)
REVERT: B   16 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8035 (p0)
REVERT: B  138 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7941 (tm-30)
REVERT: B  172 ASP cc_start: 0.8379 (t0) cc_final: 0.7806 (t0)
REVERT: B  345 MET cc_start: 0.8588 (mtt) cc_final: 0.8352 (ptt)
REVERT: B  425 GLU cc_start: 0.9223 (pm20) cc_final: 0.8922 (pm20)
  outliers start: 50
  outliers final: 45
  residues processed: 115
  average time/residue: 0.1787
  time to fit residues: 28.8503
Evaluate side-chains
  126 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 78
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 ILE
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   16 ASP
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  160 HIS
Chi-restraints excluded: chain B residue  162 LYS
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  302 LYS
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  354 LYS
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  421 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0030
   chunk 58 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0770
   overall best weight:    0.4148

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

Flipped N/Q/H residues before XYZ refinement:
A  18 GLN
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.107573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.085680 restraints weight = 18715.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 4.67
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7632  Z= 0.162
  Angle     :  0.565   7.670  10312  Z= 0.288
  Chirality :  0.044   0.207   1106
  Planarity :  0.003   0.033   1312
  Dihedral  :  6.103  53.309    998
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 26.85 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.28), residues: 900
  helix:  0.57 (0.30), residues: 315
  sheet: -1.04 (0.43), residues: 135
  loop : -1.46 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 231 
 HIS   0.003   0.001   HIS B 358 
 PHE   0.031   0.001   PHE B  60 
 TYR   0.013   0.001   TYR A 353 
 ARG   0.002   0.000   ARG A 102 

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 96
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 HIS cc_start: 0.8822 (m-70) cc_final: 0.8435 (t-170)
REVERT: A  348 GLU cc_start: 0.9432 (pp20) cc_final: 0.9230 (pp20)
REVERT: A  356 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7165 (mp0)
REVERT: A  368 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8271 (pm20)
REVERT: B   16 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.7985 (p0)
REVERT: B  138 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7910 (tm-30)
REVERT: B  172 ASP cc_start: 0.8350 (t0) cc_final: 0.7809 (t0)
REVERT: B  345 MET cc_start: 0.8553 (mtt) cc_final: 0.8304 (ptt)
REVERT: B  425 GLU cc_start: 0.9227 (pm20) cc_final: 0.8996 (pm20)
REVERT: B  426 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8360 (mp0)
  outliers start: 41
  outliers final: 34
  residues processed: 124
  average time/residue: 0.1780
  time to fit residues: 30.9505
Evaluate side-chains
  123 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 85
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   84 CYS
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    8 SER
Chi-restraints excluded: chain B residue   16 ASP
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain B residue  160 HIS
Chi-restraints excluded: chain B residue  162 LYS
Chi-restraints excluded: chain B residue  169 GLU
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  302 LYS
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  354 LYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain B residue  426 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 85 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.105931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.083886 restraints weight = 18465.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 4.60
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7632  Z= 0.200
  Angle     :  0.606   9.274  10312  Z= 0.310
  Chirality :  0.045   0.209   1106
  Planarity :  0.004   0.040   1312
  Dihedral  :  6.092  52.222    996
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 26.72 %
    Favored  : 67.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.28), residues: 900
  helix:  0.65 (0.30), residues: 309
  sheet: -1.18 (0.41), residues: 144
  loop : -1.41 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 369 
 HIS   0.003   0.001   HIS B 358 
 PHE   0.034   0.001   PHE B  60 
 TYR   0.023   0.001   TYR A 285 
 ARG   0.002   0.000   ARG A 102 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3257.56 seconds
wall clock time: 56 minutes 59.80 seconds (3419.80 seconds total)