Starting phenix.real_space_refine
on Wed Feb  4 06:22:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9sv8_55245/02_2026/9sv8_55245.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9sv8_55245/02_2026/9sv8_55245.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9sv8_55245/02_2026/9sv8_55245.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9sv8_55245/02_2026/9sv8_55245.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9sv8_55245/02_2026/9sv8_55245.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9sv8_55245/02_2026/9sv8_55245.map"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.051
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      36      5.16       5
     C    5668      2.51       5
     N    1537      2.21       5
     O    1687      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8928
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1301
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 13, 'TRANS': 152}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 4907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 628, 4907
          Classifications: {'peptide': 628}
          Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 33, 'TRANS': 590}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 2720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2720
          Classifications: {'peptide': 337}
          Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 319}
          Chain breaks: 2
  Time building chain proxies: 1.92, per 1000 atoms: 0.22
  Number of scatterers: 8928
  At special positions: 0
  Unit cell: (83.62, 95.46, 146.52, 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      36     16.00
     O    1687      8.00
     N    1537      7.00
     C    5668      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS A 113 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 537 " - pdb=" SG  CYS C 713 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 605 " - pdb=" SG  CYS B 640 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 770 " - pdb=" SG  CYS C1410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1255 " - pdb=" SG  CYS C1386 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1403 " - pdb=" SG  CYS C1408 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 282.6 milliseconds
  

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 24 sheets defined
      9.1% alpha, 40.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 279 through 281
      No H-bonds generated for 'chain 'A' and resid 279 through 281'
    Processing helix  chain 'B' and resid 55 through 59
    Processing helix  chain 'B' and resid 263 through 266
    Processing helix  chain 'B' and resid 281 through 288
      removed outlier: 3.507A  pdb=" N   LEU B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 298
    Processing helix  chain 'B' and resid 410 through 414
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 458 through 465
      removed outlier: 5.006A  pdb=" N   ALA B 463 " --> pdb=" O   ALA B 460 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE B 465 " --> pdb=" O   GLU B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 504
    Processing helix  chain 'B' and resid 578 through 584
      removed outlier: 3.551A  pdb=" N   VAL B 582 " --> pdb=" O   LYS B 578 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU B 583 " --> pdb=" O   GLY B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 601
    Processing helix  chain 'B' and resid 612 through 620
    Processing helix  chain 'C' and resid 1311 through 1320
      removed outlier: 3.553A  pdb=" N   ASN C1320 " --> pdb=" O   LYS C1316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1327 through 1332
    Processing helix  chain 'C' and resid 1334 through 1338
      removed outlier: 3.709A  pdb=" N   ASP C1337 " --> pdb=" O   ALA C1334 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ARG C1338 " --> pdb=" O   PHE C1335 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1334 through 1338'
    Processing helix  chain 'C' and resid 1394 through 1398
    Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 104
      removed outlier: 6.567A  pdb=" N   ALA A 103 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 113
      removed outlier: 3.934A  pdb=" N   CYS A 113 " --> pdb=" O   GLN A 196 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   GLN A 196 " --> pdb=" O   CYS A 113 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 241
      removed outlier: 3.505A  pdb=" N   THR A 239 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER A 295 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 276
      removed outlier: 3.644A  pdb=" N   ARG A 330 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 63
      removed outlier: 3.662A  pdb=" N   MET B   3 " --> pdb=" O   HIS B  25 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 13
      removed outlier: 6.195A  pdb=" N   LEU B  12 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   LYS B  82 " --> pdb=" O   VAL B 101 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   SER B  48 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 18
      removed outlier: 3.735A  pdb=" N   GLU B  18 " --> pdb=" O   PHE B  66 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   PHE B  66 " --> pdb=" O   GLU B  18 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 112
      removed outlier: 3.777A  pdb=" N   TYR B 125 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 117
      removed outlier: 3.712A  pdb=" N   GLY B 180 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LYS B 183 " --> pdb=" O   GLU B 146 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   VAL B 141 " --> pdb=" O   SER B 157 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   SER B 157 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL B 143 " --> pdb=" O   GLN B 155 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLN B 155 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 210 through 216
      removed outlier: 3.725A  pdb=" N   LEU B 229 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 221 through 222
      removed outlier: 3.710A  pdb=" N   VAL B 327 " --> pdb=" O   TYR B 221 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLY B 323 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   LEU B 302 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 221 through 222
      removed outlier: 3.710A  pdb=" N   VAL B 327 " --> pdb=" O   TYR B 221 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLY B 323 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   LEU B 302 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 332 through 334
    Processing sheet with id=AB5, first strand: chain 'B' and resid 341 through 342
      removed outlier: 3.828A  pdb=" N   ARG B 417 " --> pdb=" O   VAL B 402 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL B 402 " --> pdb=" O   ARG B 417 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU B 398 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 433 through 437
      removed outlier: 3.523A  pdb=" N   SER B 437 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 477 through 485
      removed outlier: 6.907A  pdb=" N   ILE B 472 " --> pdb=" O   LEU B 479 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   ALA B 481 " --> pdb=" O   TYR B 470 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   TYR B 470 " --> pdb=" O   ALA B 481 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ARG B 483 " --> pdb=" O   TYR B 468 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   TYR B 468 " --> pdb=" O   ARG B 483 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   TYR B 467 " --> pdb=" O   THR B 514 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   THR B 514 " --> pdb=" O   TYR B 467 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 541 through 545
    Processing sheet with id=AB9, first strand: chain 'C' and resid 667 through 668
      removed outlier: 3.547A  pdb=" N   ARG B 570 " --> pdb=" O   MET C 706 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY C 711 " --> pdb=" O   SER C 707 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 672 through 674
      removed outlier: 3.547A  pdb=" N   ARG B 570 " --> pdb=" O   MET C 706 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 726 through 731
      removed outlier: 3.981A  pdb=" N   VAL C 747 " --> pdb=" O   ASP C 729 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG C 745 " --> pdb=" O   ARG C 731 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 735 through 737
      removed outlier: 3.507A  pdb=" N   VAL C 828 " --> pdb=" O   GLY C 803 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 779 through 785
      removed outlier: 4.420A  pdb=" N   HIS C 779 " --> pdb=" O   LEU C 763 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASP C 820 " --> pdb=" O   ALA C 811 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 1258 through 1266
      removed outlier: 4.088A  pdb=" N   ASN C1279 " --> pdb=" O   GLN C1362 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 1324 through 1325
      removed outlier: 3.512A  pdb=" N   CYS C1386 " --> pdb=" O   VAL C1376 " (cutoff:3.500A)

    325 hydrogen bonds defined for protein.
    840 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2625
        1.33 -     1.46: 1853
        1.46 -     1.58: 4570
        1.58 -     1.71: 2
        1.71 -     1.83: 56
  Bond restraints: 9106
  Sorted by residual:
  bond pdb=" CG  PRO B  56 "
       pdb=" CD  PRO B  56 "
    ideal  model  delta    sigma   weight residual
    1.503  1.308  0.195 3.40e-02 8.65e+02 3.27e+01
  bond pdb=" N   VAL A 338 "
       pdb=" CA  VAL A 338 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.11e-02 8.12e+03 1.23e+01
  bond pdb=" CB  PRO B  56 "
       pdb=" CG  PRO B  56 "
    ideal  model  delta    sigma   weight residual
    1.492  1.667 -0.175 5.00e-02 4.00e+02 1.22e+01
  bond pdb=" N   PRO B  56 "
       pdb=" CD  PRO B  56 "
    ideal  model  delta    sigma   weight residual
    1.473  1.519 -0.046 1.40e-02 5.10e+03 1.09e+01
  bond pdb=" N   ARG B 293 "
       pdb=" CA  ARG B 293 "
    ideal  model  delta    sigma   weight residual
    1.454  1.494 -0.040 1.29e-02 6.01e+03 9.71e+00
  ... (remaining 9101 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.74: 12297
        4.74 -     9.48: 46
        9.48 -    14.23: 5
       14.23 -    18.97: 2
       18.97 -    23.71: 1
  Bond angle restraints: 12351
  Sorted by residual:
  angle pdb=" C   GLU C 655 "
        pdb=" N   GLU C 656 "
        pdb=" CA  GLU C 656 "
      ideal   model   delta    sigma   weight residual
     121.70  145.41  -23.71 1.80e+00 3.09e-01 1.74e+02
  angle pdb=" CA  PRO B  56 "
        pdb=" N   PRO B  56 "
        pdb=" CD  PRO B  56 "
      ideal   model   delta    sigma   weight residual
     112.00   94.69   17.31 1.40e+00 5.10e-01 1.53e+02
  angle pdb=" C   SER B 197 "
        pdb=" N   THR B 198 "
        pdb=" CA  THR B 198 "
      ideal   model   delta    sigma   weight residual
     121.70  136.79  -15.09 1.80e+00 3.09e-01 7.03e+01
  angle pdb=" N   PRO B  56 "
        pdb=" CD  PRO B  56 "
        pdb=" CG  PRO B  56 "
      ideal   model   delta    sigma   weight residual
     103.20   90.91   12.29 1.50e+00 4.44e-01 6.71e+01
  angle pdb=" C   LEU C1407 "
        pdb=" N   CYS C1408 "
        pdb=" CA  CYS C1408 "
      ideal   model   delta    sigma   weight residual
     120.90  110.13   10.77 1.41e+00 5.03e-01 5.84e+01
  ... (remaining 12346 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 4829
       17.83 -    35.66: 534
       35.66 -    53.49: 159
       53.49 -    71.32: 19
       71.32 -    89.15: 11
  Dihedral angle restraints: 5552
    sinusoidal: 2264
      harmonic: 3288
  Sorted by residual:
  dihedral pdb=" CD  ARG A 229 "
           pdb=" NE  ARG A 229 "
           pdb=" CZ  ARG A 229 "
           pdb=" NH1 ARG A 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   79.57  -79.57     1      1.00e+01 1.00e-02 7.86e+01
  dihedral pdb=" CD  ARG A 341 "
           pdb=" NE  ARG A 341 "
           pdb=" CZ  ARG A 341 "
           pdb=" NH1 ARG A 341 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   53.05  -53.05     1      1.00e+01 1.00e-02 3.83e+01
  dihedral pdb=" CA  TYR A 261 "
           pdb=" C   TYR A 261 "
           pdb=" N   PRO A 262 "
           pdb=" CA  PRO A 262 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.02  -27.98     0      5.00e+00 4.00e-02 3.13e+01
  ... (remaining 5549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1163
       0.062 -    0.123: 219
       0.123 -    0.185: 30
       0.185 -    0.246: 6
       0.246 -    0.308: 2
  Chirality restraints: 1420
  Sorted by residual:
  chirality pdb=" CA  ILE B 151 "
            pdb=" N   ILE B 151 "
            pdb=" C   ILE B 151 "
            pdb=" CB  ILE B 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  LEU A 339 "
            pdb=" N   LEU A 339 "
            pdb=" C   LEU A 339 "
            pdb=" CB  LEU A 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CA  GLU B 149 "
            pdb=" N   GLU B 149 "
            pdb=" C   GLU B 149 "
            pdb=" CB  GLU B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1417 not shown)

  Planarity restraints: 1587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 229 "    1.083 9.50e-02 1.11e+02   4.85e-01 1.42e+02
        pdb=" NE  ARG A 229 "   -0.065 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 229 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 229 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 229 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 341 "    0.871 9.50e-02 1.11e+02   3.90e-01 9.24e+01
        pdb=" NE  ARG A 341 "   -0.052 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 341 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 341 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 341 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 195 "   -0.789 9.50e-02 1.11e+02   3.54e-01 7.60e+01
        pdb=" NE  ARG A 195 "    0.046 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 195 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 195 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 195 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1584 not shown)

  Histogram of nonbonded interaction distances:
        1.21 -     1.95: 6
        1.95 -     2.69: 263
        2.69 -     3.43: 11440
        3.43 -     4.16: 20282
        4.16 -     4.90: 35180
  Nonbonded interactions: 67171
  Sorted by model distance:
  nonbonded pdb=" CZ3 TRP A 270 "
            pdb=" CB  VAL A 300 "
     model   vdw
     1.213 3.770
  nonbonded pdb=" OD1 ASP B 373 "
            pdb=" CG2 VAL B 375 "
     model   vdw
     1.608 3.460
  nonbonded pdb=" CZ3 TRP A 270 "
            pdb=" CG2 VAL A 300 "
     model   vdw
     1.642 3.760
  nonbonded pdb=" CD1 LEU A 339 "
            pdb=" CD  ARG A 341 "
     model   vdw
     1.764 3.860
  nonbonded pdb=" CE3 TRP A 270 "
            pdb=" CG2 VAL A 300 "
     model   vdw
     1.774 3.760
  ... (remaining 67166 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.600
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.195   9112  Z= 0.236
  Angle     :  0.860  23.710  12363  Z= 0.508
  Chirality :  0.051   0.308   1420
  Planarity :  0.019   0.485   1587
  Dihedral  : 16.218  89.150   3406
  Min Nonbonded Distance : 1.213

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.80 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.87 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.26), residues: 1105
  helix:  0.04 (0.81), residues: 46
  sheet:  0.56 (0.24), residues: 523
  loop : -0.19 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C1338 
 TYR   0.020   0.001   TYR A 260 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.036   0.002   TRP A 320 
 HIS   0.005   0.001   HIS C 765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 9106)
  covalent geometry    : angle       0.86003 (12351)
  SS BOND              : bond        0.00478 (    6)
  SS BOND              : angle       0.79896 (   12)
  hydrogen bonds       : bond        0.26809 (  301)
  hydrogen bonds       : angle       9.49228 (  840)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 217
  time to evaluate  : 0.264 
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  110 GLN cc_start: 0.7211 (pt0) cc_final: 0.6797 (pp30)
REVERT: B  142 MET cc_start: 0.6566 (tpp) cc_final: 0.6285 (mmt)
REVERT: B  151 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7432 (mm)
REVERT: B  173 ILE cc_start: 0.8462 (mm) cc_final: 0.8219 (mm)
REVERT: B  176 LEU cc_start: 0.8088 (mp) cc_final: 0.7650 (tt)
REVERT: B  194 GLN cc_start: 0.7660 (pt0) cc_final: 0.7116 (pt0)
REVERT: B  269 ILE cc_start: 0.8697 (pt) cc_final: 0.8458 (pt)
REVERT: C  685 THR cc_start: 0.7690 (p) cc_final: 0.7356 (t)
REVERT: C 1338 ARG cc_start: 0.7082 (mpp80) cc_final: 0.6542 (mmm160)
REVERT: C 1362 GLN cc_start: 0.7887 (pt0) cc_final: 0.7231 (pp30)
REVERT: C 1409 ARG cc_start: 0.6308 (ttm110) cc_final: 0.5998 (ttm-80)
  outliers start: 24
  outliers final: 2
  residues processed: 236
  average time/residue: 0.0925
  time to fit residues: 29.1102
Evaluate side-chains
  156 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 153
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  323 ASP
Chi-restraints excluded: chain B residue  151 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.3980
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    7.9990
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 241 HIS
B 190 ASN
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 ASN
C1362 GLN
** C1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.187178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.127662 restraints weight = 11536.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.131324 restraints weight = 7169.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.132591 restraints weight = 4720.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.133053 restraints weight = 4490.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.133204 restraints weight = 4218.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   9112  Z= 0.211
  Angle     :  0.713  14.250  12363  Z= 0.376
  Chirality :  0.049   0.169   1420
  Planarity :  0.005   0.067   1587
  Dihedral  :  4.884  28.038   1229
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 20.87 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.26), residues: 1105
  helix: -0.28 (0.71), residues: 53
  sheet:  0.59 (0.24), residues: 508
  loop : -0.24 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 126 
 TYR   0.027   0.002   TYR B 613 
 PHE   0.020   0.002   PHE B 237 
 TRP   0.029   0.002   TRP A 320 
 HIS   0.007   0.001   HIS C1361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 9106)
  covalent geometry    : angle       0.71251 (12351)
  SS BOND              : bond        0.00538 (    6)
  SS BOND              : angle       0.98605 (   12)
  hydrogen bonds       : bond        0.04598 (  301)
  hydrogen bonds       : angle       6.51505 (  840)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 161
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6691 (pp30)
REVERT: B   61 MET cc_start: 0.6222 (mtm) cc_final: 0.5415 (ppp)
REVERT: B  142 MET cc_start: 0.6208 (tpp) cc_final: 0.5734 (mmt)
REVERT: B  151 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7429 (mm)
REVERT: B  173 ILE cc_start: 0.8935 (mm) cc_final: 0.8650 (mm)
REVERT: B  176 LEU cc_start: 0.8215 (mp) cc_final: 0.7744 (tt)
REVERT: B  433 TYR cc_start: 0.6929 (m-10) cc_final: 0.6469 (m-80)
REVERT: B  456 ARG cc_start: 0.6548 (ttt90) cc_final: 0.6066 (ttm170)
REVERT: B  559 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7253 (ttt)
REVERT: B  583 LEU cc_start: 0.8396 (mp) cc_final: 0.8157 (mp)
REVERT: B  586 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7909 (ptmm)
REVERT: B  599 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6873 (mm-30)
REVERT: C  656 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6761 (tm-30)
REVERT: C 1297 MET cc_start: 0.8004 (ttm) cc_final: 0.7577 (ttm)
REVERT: C 1362 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7275 (pp30)
REVERT: C 1409 ARG cc_start: 0.6397 (ttm110) cc_final: 0.6096 (ttm-80)
  outliers start: 47
  outliers final: 22
  residues processed: 192
  average time/residue: 0.0807
  time to fit residues: 21.3777
Evaluate side-chains
  161 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  299 THR
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain A residue  323 ASP
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   83 PHE
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  512 TYR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  586 LYS
Chi-restraints excluded: chain C residue  657 ASN
Chi-restraints excluded: chain C residue  742 VAL
Chi-restraints excluded: chain C residue  759 VAL
Chi-restraints excluded: chain C residue  762 GLU
Chi-restraints excluded: chain C residue  802 THR
Chi-restraints excluded: chain C residue  825 SER
Chi-restraints excluded: chain C residue 1362 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:   20.0000
   chunk 51 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 ASN
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C1362 GLN
** C1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.177181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.117113 restraints weight = 11769.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.121077 restraints weight = 7008.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.123840 restraints weight = 5123.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.125086 restraints weight = 4247.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.126369 restraints weight = 3839.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.3942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   9112  Z= 0.276
  Angle     :  0.748  13.888  12363  Z= 0.391
  Chirality :  0.051   0.256   1420
  Planarity :  0.005   0.047   1587
  Dihedral  :  5.114  29.283   1228
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 21.47 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.25), residues: 1105
  helix: -0.38 (0.71), residues: 53
  sheet:  0.47 (0.24), residues: 488
  loop : -0.60 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 126 
 TYR   0.022   0.002   TYR B 470 
 PHE   0.019   0.002   PHE A 327 
 TRP   0.047   0.003   TRP A 320 
 HIS   0.008   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 ( 9106)
  covalent geometry    : angle       0.74764 (12351)
  SS BOND              : bond        0.00971 (    6)
  SS BOND              : angle       1.12389 (   12)
  hydrogen bonds       : bond        0.04794 (  301)
  hydrogen bonds       : angle       6.16937 (  840)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 144
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: B  142 MET cc_start: 0.6441 (tpp) cc_final: 0.6010 (mmt)
REVERT: B  155 GLN cc_start: 0.7553 (mt0) cc_final: 0.7269 (mp10)
REVERT: B  173 ILE cc_start: 0.9121 (mm) cc_final: 0.8836 (mm)
REVERT: B  176 LEU cc_start: 0.8247 (mp) cc_final: 0.7794 (tt)
REVERT: B  239 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8645 (p90)
REVERT: B  439 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7300 (tp)
REVERT: B  456 ARG cc_start: 0.7016 (ttt90) cc_final: 0.6602 (ttm170)
REVERT: B  586 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7967 (ptmm)
REVERT: B  599 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6848 (mm-30)
REVERT: C  712 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7823 (pt)
REVERT: C  762 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7027 (pm20)
REVERT: C  779 HIS cc_start: 0.5739 (OUTLIER) cc_final: 0.5498 (t-170)
REVERT: C 1362 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7328 (pp30)
REVERT: C 1409 ARG cc_start: 0.7256 (ttm110) cc_final: 0.6591 (ttm-80)
  outliers start: 54
  outliers final: 33
  residues processed: 188
  average time/residue: 0.0767
  time to fit residues: 20.5945
Evaluate side-chains
  165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 125
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  268 PHE
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   83 PHE
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  239 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  512 TYR
Chi-restraints excluded: chain B residue  543 VAL
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain B residue  586 LYS
Chi-restraints excluded: chain C residue  685 THR
Chi-restraints excluded: chain C residue  698 THR
Chi-restraints excluded: chain C residue  712 ILE
Chi-restraints excluded: chain C residue  730 LEU
Chi-restraints excluded: chain C residue  742 VAL
Chi-restraints excluded: chain C residue  747 VAL
Chi-restraints excluded: chain C residue  759 VAL
Chi-restraints excluded: chain C residue  762 GLU
Chi-restraints excluded: chain C residue  779 HIS
Chi-restraints excluded: chain C residue  798 VAL
Chi-restraints excluded: chain C residue  802 THR
Chi-restraints excluded: chain C residue  825 SER
Chi-restraints excluded: chain C residue 1331 LEU
Chi-restraints excluded: chain C residue 1356 LEU
Chi-restraints excluded: chain C residue 1362 GLN
Chi-restraints excluded: chain C residue 1387 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 19 optimal weight:   20.0000
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 49 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 58 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
B 104 GLN
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1370 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 = 0.4260 r_free = 0.4260 target = 0.180648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.120464 restraints weight = 11849.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.124870 restraints weight = 6773.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.127746 restraints weight = 4843.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.129482 restraints weight = 3960.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.130711 restraints weight = 3513.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9112  Z= 0.136
  Angle     :  0.628  13.786  12363  Z= 0.327
  Chirality :  0.047   0.152   1420
  Planarity :  0.005   0.071   1587
  Dihedral  :  4.682  29.551   1224
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 22.56 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.25), residues: 1105
  helix: -0.12 (0.76), residues: 53
  sheet:  0.53 (0.23), residues: 497
  loop : -0.41 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B  13 
 TYR   0.031   0.002   TYR B 613 
 PHE   0.021   0.001   PHE C1364 
 TRP   0.050   0.003   TRP A 320 
 HIS   0.004   0.001   HIS B 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9106)
  covalent geometry    : angle       0.62688 (12351)
  SS BOND              : bond        0.00482 (    6)
  SS BOND              : angle       1.13457 (   12)
  hydrogen bonds       : bond        0.03512 (  301)
  hydrogen bonds       : angle       5.70190 (  840)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 140
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.6518 (mtm) cc_final: 0.6162 (ppp)
REVERT: B  142 MET cc_start: 0.6270 (tpp) cc_final: 0.5888 (mmt)
REVERT: B  151 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7200 (mm)
REVERT: B  155 GLN cc_start: 0.7615 (mt0) cc_final: 0.7253 (mp10)
REVERT: B  173 ILE cc_start: 0.9116 (mm) cc_final: 0.8913 (mm)
REVERT: B  176 LEU cc_start: 0.8136 (mp) cc_final: 0.7776 (tt)
REVERT: B  439 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7331 (tp)
REVERT: B  456 ARG cc_start: 0.6992 (ttt90) cc_final: 0.6593 (ttm170)
REVERT: B  586 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7846 (ptmm)
REVERT: B  587 ASN cc_start: 0.8329 (m110) cc_final: 0.7915 (m110)
REVERT: B  599 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6815 (mm-30)
REVERT: C  712 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7673 (pt)
REVERT: C  740 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.5936 (mp0)
REVERT: C  762 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6979 (pm20)
REVERT: C 1409 ARG cc_start: 0.7240 (ttm110) cc_final: 0.6802 (ptm160)
  outliers start: 39
  outliers final: 23
  residues processed: 167
  average time/residue: 0.0837
  time to fit residues: 20.0678
Evaluate side-chains
  158 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   83 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  512 TYR
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain B residue  586 LYS
Chi-restraints excluded: chain C residue  712 ILE
Chi-restraints excluded: chain C residue  730 LEU
Chi-restraints excluded: chain C residue  740 GLU
Chi-restraints excluded: chain C residue  742 VAL
Chi-restraints excluded: chain C residue  762 GLU
Chi-restraints excluded: chain C residue  802 THR
Chi-restraints excluded: chain C residue  825 SER
Chi-restraints excluded: chain C residue 1323 ASP
Chi-restraints excluded: chain C residue 1393 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C1370 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 = 0.4234 r_free = 0.4234 target = 0.178208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.118612 restraints weight = 11715.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.122902 restraints weight = 6715.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.125699 restraints weight = 4817.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.127437 restraints weight = 3941.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.128400 restraints weight = 3496.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9112  Z= 0.174
  Angle     :  0.642  13.743  12363  Z= 0.333
  Chirality :  0.048   0.158   1420
  Planarity :  0.005   0.036   1587
  Dihedral  :  4.635  27.568   1224
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 22.96 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.25), residues: 1105
  helix: -0.07 (0.75), residues: 53
  sheet:  0.43 (0.23), residues: 506
  loop : -0.38 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  13 
 TYR   0.027   0.002   TYR A 260 
 PHE   0.014   0.002   PHE C1364 
 TRP   0.036   0.003   TRP A 320 
 HIS   0.004   0.001   HIS C 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 9106)
  covalent geometry    : angle       0.64098 (12351)
  SS BOND              : bond        0.00473 (    6)
  SS BOND              : angle       1.05670 (   12)
  hydrogen bonds       : bond        0.03559 (  301)
  hydrogen bonds       : angle       5.52153 (  840)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 136
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.6785 (mtm) cc_final: 0.6486 (ppp)
REVERT: B  142 MET cc_start: 0.6345 (tpp) cc_final: 0.5901 (mmt)
REVERT: B  147 ASN cc_start: 0.6959 (m-40) cc_final: 0.6658 (m-40)
REVERT: B  155 GLN cc_start: 0.7640 (mt0) cc_final: 0.7176 (mp10)
REVERT: B  173 ILE cc_start: 0.9151 (mm) cc_final: 0.8935 (mm)
REVERT: B  176 LEU cc_start: 0.8132 (mp) cc_final: 0.7794 (tt)
REVERT: B  219 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7696 (mtmm)
REVERT: B  439 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7400 (tp)
REVERT: B  456 ARG cc_start: 0.7077 (ttt90) cc_final: 0.6665 (ttm170)
REVERT: B  586 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7801 (ptmm)
REVERT: B  587 ASN cc_start: 0.8328 (m110) cc_final: 0.7820 (m110)
REVERT: B  599 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6840 (mm-30)
REVERT: C  712 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7722 (pt)
REVERT: C  740 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6133 (mp0)
REVERT: C  762 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7035 (pm20)
REVERT: C 1297 MET cc_start: 0.8012 (ttm) cc_final: 0.7705 (ttm)
  outliers start: 50
  outliers final: 35
  residues processed: 172
  average time/residue: 0.0832
  time to fit residues: 20.5308
Evaluate side-chains
  166 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 126
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   83 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  316 MET
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  512 TYR
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  543 VAL
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  586 LYS
Chi-restraints excluded: chain C residue  685 THR
Chi-restraints excluded: chain C residue  712 ILE
Chi-restraints excluded: chain C residue  730 LEU
Chi-restraints excluded: chain C residue  740 GLU
Chi-restraints excluded: chain C residue  742 VAL
Chi-restraints excluded: chain C residue  747 VAL
Chi-restraints excluded: chain C residue  762 GLU
Chi-restraints excluded: chain C residue  802 THR
Chi-restraints excluded: chain C residue  825 SER
Chi-restraints excluded: chain C residue 1323 ASP
Chi-restraints excluded: chain C residue 1393 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 83 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 108 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1370 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 = 0.4225 r_free = 0.4225 target = 0.177473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.117493 restraints weight = 11806.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.121640 restraints weight = 6920.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.124383 restraints weight = 5042.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.126118 restraints weight = 4156.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.127032 restraints weight = 3703.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.5083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9112  Z= 0.193
  Angle     :  0.662  14.787  12363  Z= 0.345
  Chirality :  0.048   0.178   1420
  Planarity :  0.005   0.040   1587
  Dihedral  :  4.708  27.092   1224
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 22.37 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.25), residues: 1105
  helix: -0.25 (0.73), residues: 53
  sheet:  0.35 (0.23), residues: 505
  loop : -0.35 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 126 
 TYR   0.027   0.002   TYR A 260 
 PHE   0.014   0.002   PHE B 624 
 TRP   0.057   0.003   TRP A 320 
 HIS   0.005   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 9106)
  covalent geometry    : angle       0.66125 (12351)
  SS BOND              : bond        0.00434 (    6)
  SS BOND              : angle       1.00543 (   12)
  hydrogen bonds       : bond        0.03586 (  301)
  hydrogen bonds       : angle       5.53709 (  840)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 137
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 PHE cc_start: 0.7211 (m-10) cc_final: 0.6944 (m-80)
REVERT: A  318 LEU cc_start: 0.8625 (mt) cc_final: 0.8276 (mt)
REVERT: B   44 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7175 (tppt)
REVERT: B   61 MET cc_start: 0.6871 (mtm) cc_final: 0.6547 (ppp)
REVERT: B  142 MET cc_start: 0.6369 (tpp) cc_final: 0.5921 (mmt)
REVERT: B  155 GLN cc_start: 0.7766 (mt0) cc_final: 0.7359 (mp10)
REVERT: B  173 ILE cc_start: 0.9167 (mm) cc_final: 0.8961 (mm)
REVERT: B  176 LEU cc_start: 0.8155 (mp) cc_final: 0.7834 (tt)
REVERT: B  219 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7668 (mtmm)
REVERT: B  439 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7512 (tp)
REVERT: B  456 ARG cc_start: 0.7173 (ttt90) cc_final: 0.6718 (ttm170)
REVERT: B  530 TRP cc_start: 0.8426 (t60) cc_final: 0.7661 (t60)
REVERT: B  586 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7792 (ptmm)
REVERT: B  587 ASN cc_start: 0.8343 (m110) cc_final: 0.7766 (m110)
REVERT: B  599 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6817 (mm-30)
REVERT: C  712 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7686 (pt)
REVERT: C  740 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6237 (mp0)
REVERT: C  762 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6996 (pm20)
  outliers start: 55
  outliers final: 45
  residues processed: 176
  average time/residue: 0.0818
  time to fit residues: 21.3051
Evaluate side-chains
  179 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 128
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   83 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  316 MET
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  512 TYR
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  543 VAL
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  586 LYS
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain C residue  685 THR
Chi-restraints excluded: chain C residue  712 ILE
Chi-restraints excluded: chain C residue  730 LEU
Chi-restraints excluded: chain C residue  740 GLU
Chi-restraints excluded: chain C residue  742 VAL
Chi-restraints excluded: chain C residue  747 VAL
Chi-restraints excluded: chain C residue  762 GLU
Chi-restraints excluded: chain C residue  802 THR
Chi-restraints excluded: chain C residue  825 SER
Chi-restraints excluded: chain C residue 1323 ASP
Chi-restraints excluded: chain C residue 1393 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0980
   chunk 107 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 19 optimal weight:   20.0000
   chunk 109 optimal weight:    0.0980
   chunk 29 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 74 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 GLN
C 755 GLN
** C1370 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 = 0.4257 r_free = 0.4257 target = 0.180289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.120745 restraints weight = 11717.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.125229 restraints weight = 6670.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.128145 restraints weight = 4736.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.129919 restraints weight = 3871.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.130751 restraints weight = 3431.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.5211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9112  Z= 0.118
  Angle     :  0.603  13.411  12363  Z= 0.314
  Chirality :  0.046   0.163   1420
  Planarity :  0.004   0.040   1587
  Dihedral  :  4.460  25.484   1224
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 23.46 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.25), residues: 1105
  helix:  0.11 (0.78), residues: 53
  sheet:  0.52 (0.23), residues: 501
  loop : -0.27 (0.26), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1288 
 TYR   0.024   0.001   TYR A 260 
 PHE   0.014   0.001   PHE B 624 
 TRP   0.038   0.002   TRP A 320 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9106)
  covalent geometry    : angle       0.60325 (12351)
  SS BOND              : bond        0.00391 (    6)
  SS BOND              : angle       0.75534 (   12)
  hydrogen bonds       : bond        0.03106 (  301)
  hydrogen bonds       : angle       5.28654 (  840)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 132
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 PHE cc_start: 0.7131 (m-10) cc_final: 0.6860 (m-80)
REVERT: A  318 LEU cc_start: 0.8482 (mt) cc_final: 0.8118 (mt)
REVERT: B   44 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7124 (tppt)
REVERT: B   61 MET cc_start: 0.6832 (mtm) cc_final: 0.6624 (tmm)
REVERT: B  142 MET cc_start: 0.6264 (tpp) cc_final: 0.5905 (mmt)
REVERT: B  155 GLN cc_start: 0.7731 (mt0) cc_final: 0.7355 (mp10)
REVERT: B  176 LEU cc_start: 0.8099 (mp) cc_final: 0.7844 (tt)
REVERT: B  219 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7627 (mtmm)
REVERT: B  439 LEU cc_start: 0.8043 (mp) cc_final: 0.7497 (tp)
REVERT: B  456 ARG cc_start: 0.7244 (ttt90) cc_final: 0.6846 (ttm170)
REVERT: B  530 TRP cc_start: 0.8373 (t60) cc_final: 0.7521 (t60)
REVERT: B  586 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7735 (ptmm)
REVERT: B  587 ASN cc_start: 0.8264 (m110) cc_final: 0.7659 (m110)
REVERT: B  599 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6848 (mm-30)
REVERT: C  712 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7705 (pt)
REVERT: C  723 MET cc_start: 0.7204 (tpp) cc_final: 0.6817 (mmt)
REVERT: C  740 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6290 (mp0)
REVERT: C  762 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7066 (pm20)
  outliers start: 50
  outliers final: 34
  residues processed: 167
  average time/residue: 0.0821
  time to fit residues: 20.2366
Evaluate side-chains
  167 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 128
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   83 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  316 MET
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  512 TYR
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  586 LYS
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain C residue  685 THR
Chi-restraints excluded: chain C residue  712 ILE
Chi-restraints excluded: chain C residue  730 LEU
Chi-restraints excluded: chain C residue  740 GLU
Chi-restraints excluded: chain C residue  742 VAL
Chi-restraints excluded: chain C residue  747 VAL
Chi-restraints excluded: chain C residue  762 GLU
Chi-restraints excluded: chain C residue  825 SER
Chi-restraints excluded: chain C residue 1323 ASP
Chi-restraints excluded: chain C residue 1387 THR
Chi-restraints excluded: chain C residue 1393 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 4 optimal weight:   10.0000
   chunk 96 optimal weight:    0.3980
   chunk 103 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 19 optimal weight:   20.0000
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 GLN
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1365 ASN
** C1370 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 = 0.4244 r_free = 0.4244 target = 0.179467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.119731 restraints weight = 11593.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.124104 restraints weight = 6638.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.126914 restraints weight = 4761.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.128852 restraints weight = 3903.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.129858 restraints weight = 3458.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.5376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9112  Z= 0.141
  Angle     :  0.625  13.479  12363  Z= 0.324
  Chirality :  0.047   0.235   1420
  Planarity :  0.004   0.040   1587
  Dihedral  :  4.438  24.160   1224
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 24.06 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.25), residues: 1105
  helix:  0.01 (0.76), residues: 53
  sheet:  0.46 (0.23), residues: 509
  loop : -0.25 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 322 
 TYR   0.024   0.001   TYR A 260 
 PHE   0.018   0.001   PHE B 196 
 TRP   0.023   0.002   TRP A 320 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 9106)
  covalent geometry    : angle       0.62475 (12351)
  SS BOND              : bond        0.00394 (    6)
  SS BOND              : angle       0.77011 (   12)
  hydrogen bonds       : bond        0.03213 (  301)
  hydrogen bonds       : angle       5.23903 (  840)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 134
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 PHE cc_start: 0.7119 (m-10) cc_final: 0.6855 (m-80)
REVERT: A  318 LEU cc_start: 0.8560 (mt) cc_final: 0.8217 (mt)
REVERT: B   44 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7138 (tppt)
REVERT: B  142 MET cc_start: 0.6326 (tpp) cc_final: 0.5956 (mmt)
REVERT: B  176 LEU cc_start: 0.8109 (mp) cc_final: 0.7876 (tt)
REVERT: B  219 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7612 (mtmm)
REVERT: B  439 LEU cc_start: 0.8060 (mp) cc_final: 0.7513 (tp)
REVERT: B  530 TRP cc_start: 0.8425 (t60) cc_final: 0.7574 (t60)
REVERT: B  586 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7740 (ptmm)
REVERT: B  587 ASN cc_start: 0.8241 (m110) cc_final: 0.7599 (m110)
REVERT: B  599 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6849 (mm-30)
REVERT: C  740 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6316 (mp0)
REVERT: C  762 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7049 (pm20)
REVERT: C 1338 ARG cc_start: 0.7770 (mpp80) cc_final: 0.7466 (mpp80)
  outliers start: 44
  outliers final: 34
  residues processed: 166
  average time/residue: 0.0743
  time to fit residues: 18.0534
Evaluate side-chains
  161 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 123
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   83 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  316 MET
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  512 TYR
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  586 LYS
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain C residue  685 THR
Chi-restraints excluded: chain C residue  730 LEU
Chi-restraints excluded: chain C residue  740 GLU
Chi-restraints excluded: chain C residue  742 VAL
Chi-restraints excluded: chain C residue  747 VAL
Chi-restraints excluded: chain C residue  762 GLU
Chi-restraints excluded: chain C residue  825 SER
Chi-restraints excluded: chain C residue 1323 ASP
Chi-restraints excluded: chain C residue 1387 THR
Chi-restraints excluded: chain C residue 1393 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 19 optimal weight:   20.0000
   chunk 101 optimal weight:    3.9990
   chunk 2 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   chunk 100 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1365 ASN
** C1370 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 = 0.4209 r_free = 0.4209 target = 0.176514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.116504 restraints weight = 11775.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.120619 restraints weight = 6922.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.123238 restraints weight = 5040.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.125011 restraints weight = 4185.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.125914 restraints weight = 3726.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.5695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9112  Z= 0.214
  Angle     :  0.688  13.715  12363  Z= 0.354
  Chirality :  0.049   0.244   1420
  Planarity :  0.005   0.041   1587
  Dihedral  :  4.708  26.406   1224
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 24.65 %
    Favored  : 70.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.25), residues: 1105
  helix: -0.01 (0.76), residues: 53
  sheet:  0.36 (0.23), residues: 493
  loop : -0.39 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 126 
 TYR   0.027   0.002   TYR A 260 
 PHE   0.015   0.002   PHE C1358 
 TRP   0.026   0.002   TRP B 182 
 HIS   0.005   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 9106)
  covalent geometry    : angle       0.68726 (12351)
  SS BOND              : bond        0.00483 (    6)
  SS BOND              : angle       0.92200 (   12)
  hydrogen bonds       : bond        0.03700 (  301)
  hydrogen bonds       : angle       5.43393 (  840)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 136
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 PHE cc_start: 0.7113 (m-10) cc_final: 0.6817 (m-80)
REVERT: A  318 LEU cc_start: 0.8573 (mt) cc_final: 0.8260 (mt)
REVERT: B   44 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7146 (tppt)
REVERT: B  142 MET cc_start: 0.6503 (tpp) cc_final: 0.6051 (mmt)
REVERT: B  145 ILE cc_start: 0.8758 (mt) cc_final: 0.8542 (mm)
REVERT: B  219 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7600 (mtmm)
REVERT: B  440 ARG cc_start: 0.7556 (tpm170) cc_final: 0.6805 (tpm170)
REVERT: B  456 ARG cc_start: 0.7337 (ttt90) cc_final: 0.6765 (ttm170)
REVERT: B  530 TRP cc_start: 0.8493 (t60) cc_final: 0.7788 (t60)
REVERT: B  586 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7800 (ptmm)
REVERT: B  587 ASN cc_start: 0.8254 (m110) cc_final: 0.7555 (m110)
REVERT: B  599 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6956 (mm-30)
REVERT: C  723 MET cc_start: 0.7187 (tpp) cc_final: 0.6737 (mmt)
REVERT: C  740 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6638 (mp0)
REVERT: C  801 LYS cc_start: 0.7860 (mttt) cc_final: 0.7438 (mtmm)
REVERT: C 1338 ARG cc_start: 0.7789 (mpp80) cc_final: 0.7479 (mpp80)
  outliers start: 44
  outliers final: 35
  residues processed: 167
  average time/residue: 0.0740
  time to fit residues: 17.7405
Evaluate side-chains
  164 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 126
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   83 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  316 MET
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  512 TYR
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  543 VAL
Chi-restraints excluded: chain B residue  586 LYS
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain C residue  685 THR
Chi-restraints excluded: chain C residue  730 LEU
Chi-restraints excluded: chain C residue  740 GLU
Chi-restraints excluded: chain C residue  742 VAL
Chi-restraints excluded: chain C residue  747 VAL
Chi-restraints excluded: chain C residue  762 GLU
Chi-restraints excluded: chain C residue  825 SER
Chi-restraints excluded: chain C residue 1323 ASP
Chi-restraints excluded: chain C residue 1387 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 110 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1370 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 = 0.4233 r_free = 0.4233 target = 0.178822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.119112 restraints weight = 11536.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.123441 restraints weight = 6627.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.126262 restraints weight = 4755.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.127970 restraints weight = 3906.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.128908 restraints weight = 3474.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.5811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9112  Z= 0.145
  Angle     :  0.652  13.475  12363  Z= 0.331
  Chirality :  0.047   0.190   1420
  Planarity :  0.005   0.053   1587
  Dihedral  :  4.522  24.909   1224
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.85 %
    Favored  : 70.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.25), residues: 1105
  helix:  0.06 (0.76), residues: 53
  sheet:  0.33 (0.23), residues: 507
  loop : -0.33 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 126 
 TYR   0.025   0.001   TYR A 260 
 PHE   0.011   0.001   PHE C1358 
 TRP   0.020   0.002   TRP B 182 
 HIS   0.005   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9106)
  covalent geometry    : angle       0.65154 (12351)
  SS BOND              : bond        0.00382 (    6)
  SS BOND              : angle       0.77598 (   12)
  hydrogen bonds       : bond        0.03227 (  301)
  hydrogen bonds       : angle       5.25093 (  840)

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

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

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 132
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7562 (t)
REVERT: A  278 PHE cc_start: 0.7202 (m-10) cc_final: 0.6934 (m-80)
REVERT: A  318 LEU cc_start: 0.8473 (mt) cc_final: 0.8154 (mt)
REVERT: B   44 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7162 (tppt)
REVERT: B  142 MET cc_start: 0.6377 (tpp) cc_final: 0.5997 (mmt)
REVERT: B  219 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7597 (mtmm)
REVERT: B  349 ASP cc_start: 0.7986 (m-30) cc_final: 0.7670 (m-30)
REVERT: B  440 ARG cc_start: 0.7538 (tpm170) cc_final: 0.6818 (tpm170)
REVERT: B  530 TRP cc_start: 0.8455 (t60) cc_final: 0.7703 (t60)
REVERT: B  586 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7852 (ptmm)
REVERT: B  599 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6859 (mm-30)
REVERT: C  723 MET cc_start: 0.7225 (tpp) cc_final: 0.6854 (mmt)
REVERT: C  740 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6463 (mp0)
REVERT: C  762 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6998 (pm20)
REVERT: C 1338 ARG cc_start: 0.7757 (mpp80) cc_final: 0.7473 (mpp80)
  outliers start: 42
  outliers final: 36
  residues processed: 163
  average time/residue: 0.0830
  time to fit residues: 19.6875
Evaluate side-chains
  168 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 127
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 SER
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  113 CYS
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  206 GLU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   83 PHE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  213 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  316 MET
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  369 VAL
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  512 TYR
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  543 VAL
Chi-restraints excluded: chain B residue  554 VAL
Chi-restraints excluded: chain B residue  586 LYS
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain C residue  685 THR
Chi-restraints excluded: chain C residue  730 LEU
Chi-restraints excluded: chain C residue  740 GLU
Chi-restraints excluded: chain C residue  742 VAL
Chi-restraints excluded: chain C residue  747 VAL
Chi-restraints excluded: chain C residue  762 GLU
Chi-restraints excluded: chain C residue  825 SER
Chi-restraints excluded: chain C residue 1323 ASP
Chi-restraints excluded: chain C residue 1387 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 52 optimal weight:    0.4980
   chunk 76 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 60 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 630 GLN
** C1370 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 = 0.4275 r_free = 0.4275 target = 0.182613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.122710 restraints weight = 11423.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.127297 restraints weight = 6373.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.130311 restraints weight = 4520.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.132053 restraints weight = 3688.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.133236 restraints weight = 3282.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.5915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9112  Z= 0.123
  Angle     :  0.632  13.315  12363  Z= 0.318
  Chirality :  0.047   0.204   1420
  Planarity :  0.004   0.045   1587
  Dihedral  :  4.310  23.834   1224
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 24.95 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.25), residues: 1105
  helix:  0.26 (0.78), residues: 53
  sheet:  0.46 (0.23), residues: 501
  loop : -0.38 (0.26), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C1288 
 TYR   0.022   0.001   TYR A 260 
 PHE   0.013   0.001   PHE C1364 
 TRP   0.015   0.002   TRP B 182 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9106)
  covalent geometry    : angle       0.63204 (12351)
  SS BOND              : bond        0.00401 (    6)
  SS BOND              : angle       0.69394 (   12)
  hydrogen bonds       : bond        0.03029 (  301)
  hydrogen bonds       : angle       5.07180 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1893.27 seconds
wall clock time: 33 minutes 12.30 seconds (1992.30 seconds total)