Starting phenix.real_space_refine
on Wed Jan 15 20:20:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rga_19131/01_2025/8rga_19131.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rga_19131/01_2025/8rga_19131.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rga_19131/01_2025/8rga_19131.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rga_19131/01_2025/8rga_19131.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rga_19131/01_2025/8rga_19131.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rga_19131/01_2025/8rga_19131.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.024
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    5650      2.51       5
     N    1468      2.21       5
     O    1648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8802
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4401
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 17, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 4401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4401
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 17, 'TRANS': 554}
  Time building chain proxies: 5.48, per 1000 atoms: 0.62
  Number of scatterers: 8802
  At special positions: 0
  Unit cell: (71.315, 113.265, 132.562, 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    1648      8.00
     N    1468      7.00
     C    5650      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.36
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 4 sheets defined
      68.1% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 21
    Processing helix  chain 'A' and resid 26 through 56
      Proline residue:  A  47  - end of helix
    Processing helix  chain 'A' and resid 62 through 110
      removed outlier: 3.707A  pdb=" N   GLN A  66 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 119
      removed outlier: 3.874A  pdb=" N   ALA A 119 " --> pdb=" O   PHE A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 140
    Processing helix  chain 'A' and resid 140 through 163
    Processing helix  chain 'A' and resid 165 through 174
      removed outlier: 3.511A  pdb=" N   VAL A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 210
      Proline residue:  A 183  - end of helix
    Processing helix  chain 'A' and resid 212 through 220
    Processing helix  chain 'A' and resid 221 through 275
      Proline residue:  A 252  - end of helix
      removed outlier: 3.824A  pdb=" N   SER A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 295
    Processing helix  chain 'A' and resid 295 through 322
      removed outlier: 4.497A  pdb=" N   GLN A 299 " --> pdb=" O   MET A 295 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN A 308 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLY A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 387
    Processing helix  chain 'A' and resid 409 through 416
    Processing helix  chain 'A' and resid 430 through 437
    Processing helix  chain 'A' and resid 447 through 455
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.710A  pdb=" N   ARG A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ASN A 496 " --> pdb=" O   ALA A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 525
    Processing helix  chain 'A' and resid 537 through 542
      removed outlier: 3.893A  pdb=" N   VAL A 541 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ASP A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 537 through 542'
    Processing helix  chain 'A' and resid 560 through 567
    Processing helix  chain 'A' and resid 570 through 581
    Processing helix  chain 'B' and resid 12 through 21
    Processing helix  chain 'B' and resid 26 through 57
      Proline residue:  B  47  - end of helix
    Processing helix  chain 'B' and resid 60 through 110
    Processing helix  chain 'B' and resid 112 through 119
      removed outlier: 3.774A  pdb=" N   ASP B 116 " --> pdb=" O   VAL B 112 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA B 119 " --> pdb=" O   PHE B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 140
      removed outlier: 4.021A  pdb=" N   ASP B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   THR B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 163
    Processing helix  chain 'B' and resid 165 through 174
      removed outlier: 3.500A  pdb=" N   VAL B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 210
      Proline residue:  B 183  - end of helix
    Processing helix  chain 'B' and resid 212 through 219
    Processing helix  chain 'B' and resid 221 through 275
      removed outlier: 3.615A  pdb=" N   GLU B 225 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   LEU B 249 " --> pdb=" O   LYS B 245 " (cutoff:3.500A)
      Proline residue:  B 252  - end of helix
    Processing helix  chain 'B' and resid 281 through 295
    Processing helix  chain 'B' and resid 296 through 321
      removed outlier: 4.401A  pdb=" N   GLN B 308 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LYS B 309 " --> pdb=" O   THR B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 388
    Processing helix  chain 'B' and resid 403 through 407
    Processing helix  chain 'B' and resid 409 through 416
      removed outlier: 3.504A  pdb=" N   ARG B 414 " --> pdb=" O   LEU B 410 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   HIS B 416 " --> pdb=" O   SER B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 437
    Processing helix  chain 'B' and resid 447 through 455
    Processing helix  chain 'B' and resid 480 through 496
      removed outlier: 3.642A  pdb=" N   ARG B 484 " --> pdb=" O   SER B 480 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ASN B 496 " --> pdb=" O   ALA B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 525
      removed outlier: 4.116A  pdb=" N   SER B 516 " --> pdb=" O   GLN B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 567
    Processing helix  chain 'B' and resid 570 through 581
    Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364
      removed outlier: 7.466A  pdb=" N   ALA A 362 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   ASP A 344 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ILE A 364 " --> pdb=" O   GLN A 342 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   GLN A 342 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 420
      removed outlier: 5.832A  pdb=" N   GLY A 418 " --> pdb=" O   MET A 501 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   THR A 370 " --> pdb=" O   VAL A 532 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   VAL A 369 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   LEU A 547 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ALA A 371 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   VAL A 549 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 364
      removed outlier: 7.667A  pdb=" N   ALA B 362 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 5.410A  pdb=" N   ASP B 344 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ILE B 364 " --> pdb=" O   GLN B 342 " (cutoff:3.500A)
      removed outlier: 4.812A  pdb=" N   GLN B 342 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 418
      removed outlier: 3.719A  pdb=" N   GLY B 418 " --> pdb=" O   ILE B 499 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   MET B 501 " --> pdb=" O   GLY B 418 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   THR B 370 " --> pdb=" O   VAL B 532 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   VAL B 369 " --> pdb=" O   GLN B 545 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   LEU B 547 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ALA B 371 " --> pdb=" O   LEU B 547 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   VAL B 549 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU B 546 " --> pdb=" O   ARG B 557 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   ARG B 557 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   PHE B 548 " --> pdb=" O   THR B 555 " (cutoff:3.500A)

    592 hydrogen bonds defined for protein.
    1752 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.44

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1452
        1.31 -     1.44: 2161
        1.44 -     1.57: 5252
        1.57 -     1.69: 1
        1.69 -     1.82: 70
  Bond restraints: 8936
  Sorted by residual:
  bond pdb=" C   SER A 511 "
       pdb=" O   SER A 511 "
    ideal  model  delta    sigma   weight residual
    1.236  1.185  0.051 1.21e-02 6.83e+03 1.77e+01
  bond pdb=" CG  PRO A 175 "
       pdb=" CD  PRO A 175 "
    ideal  model  delta    sigma   weight residual
    1.503  1.364  0.139 3.40e-02 8.65e+02 1.67e+01
  bond pdb=" CB  PRO A 175 "
       pdb=" CG  PRO A 175 "
    ideal  model  delta    sigma   weight residual
    1.492  1.652 -0.160 5.00e-02 4.00e+02 1.03e+01
  bond pdb=" N   ASP B 510 "
       pdb=" CA  ASP B 510 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.29e-02 6.01e+03 8.97e+00
  bond pdb=" N   ASP A 510 "
       pdb=" CA  ASP A 510 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.29e-02 6.01e+03 8.13e+00
  ... (remaining 8931 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.64: 11947
        3.64 -     7.27: 125
        7.27 -    10.91: 19
       10.91 -    14.55: 1
       14.55 -    18.19: 2
  Bond angle restraints: 12094
  Sorted by residual:
  angle pdb=" CA  PRO A 175 "
        pdb=" N   PRO A 175 "
        pdb=" CD  PRO A 175 "
      ideal   model   delta    sigma   weight residual
     112.00   93.81   18.19 1.40e+00 5.10e-01 1.69e+02
  angle pdb=" N   PRO A 175 "
        pdb=" CD  PRO A 175 "
        pdb=" CG  PRO A 175 "
      ideal   model   delta    sigma   weight residual
     103.20   92.20   11.00 1.50e+00 4.44e-01 5.37e+01
  angle pdb=" CA  PRO B 404 "
        pdb=" N   PRO B 404 "
        pdb=" CD  PRO B 404 "
      ideal   model   delta    sigma   weight residual
     112.00  103.96    8.04 1.40e+00 5.10e-01 3.30e+01
  angle pdb=" N   ALA A 505 "
        pdb=" CA  ALA A 505 "
        pdb=" C   ALA A 505 "
      ideal   model   delta    sigma   weight residual
     113.19  106.95    6.24 1.19e+00 7.06e-01 2.75e+01
  angle pdb=" N   PRO B 404 "
        pdb=" CA  PRO B 404 "
        pdb=" C   PRO B 404 "
      ideal   model   delta    sigma   weight residual
     112.47  102.07   10.40 2.06e+00 2.36e-01 2.55e+01
  ... (remaining 12089 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 4633
       17.25 -    34.50: 602
       34.50 -    51.75: 138
       51.75 -    69.00: 24
       69.00 -    86.25: 11
  Dihedral angle restraints: 5408
    sinusoidal: 2132
      harmonic: 3276
  Sorted by residual:
  dihedral pdb=" C   GLU B 403 "
           pdb=" N   GLU B 403 "
           pdb=" CA  GLU B 403 "
           pdb=" CB  GLU B 403 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.39   16.79     0      2.50e+00 1.60e-01 4.51e+01
  dihedral pdb=" N   GLU B 403 "
           pdb=" C   GLU B 403 "
           pdb=" CA  GLU B 403 "
           pdb=" CB  GLU B 403 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.07  -16.27     0      2.50e+00 1.60e-01 4.23e+01
  dihedral pdb=" CA  GLY B 401 "
           pdb=" C   GLY B 401 "
           pdb=" N   ASP B 402 "
           pdb=" CA  ASP B 402 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.00   28.00     0      5.00e+00 4.00e-02 3.14e+01
  ... (remaining 5405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 1429
       0.122 -    0.244: 34
       0.244 -    0.366: 0
       0.366 -    0.487: 0
       0.487 -    0.609: 1
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CA  GLU B 403 "
            pdb=" N   GLU B 403 "
            pdb=" C   GLU B 403 "
            pdb=" CB  GLU B 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.90    0.61 2.00e-01 2.50e+01 9.28e+00
  chirality pdb=" CA  ASP B 510 "
            pdb=" N   ASP B 510 "
            pdb=" C   ASP B 510 "
            pdb=" CB  ASP B 510 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  LEU B 439 "
            pdb=" N   LEU B 439 "
            pdb=" C   LEU B 439 "
            pdb=" CB  LEU B 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 1461 not shown)

  Planarity restraints: 1518
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 174 "   -0.108 5.00e-02 4.00e+02   1.49e-01 3.53e+01
        pdb=" N   PRO A 175 "    0.256 5.00e-02 4.00e+02
        pdb=" CA  PRO A 175 "   -0.071 5.00e-02 4.00e+02
        pdb=" CD  PRO A 175 "   -0.077 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 403 "   -0.023 2.00e-02 2.50e+03   4.38e-02 1.92e+01
        pdb=" C   GLU B 403 "    0.076 2.00e-02 2.50e+03
        pdb=" O   GLU B 403 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   PRO B 404 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 403 "   -0.060 5.00e-02 4.00e+02   8.68e-02 1.21e+01
        pdb=" N   PRO B 404 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO B 404 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 404 "   -0.047 5.00e-02 4.00e+02
  ... (remaining 1515 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 116
        2.65 -     3.21: 8892
        3.21 -     3.78: 14091
        3.78 -     4.34: 17511
        4.34 -     4.90: 28388
  Nonbonded interactions: 68998
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  40 "
            pdb=" OG1 THR B 147 "
     model   vdw
     2.091 3.040
  nonbonded pdb=" N   GLU B 222 "
            pdb=" OE1 GLU B 222 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OH  TYR A 226 "
            pdb=" OE1 GLU B 101 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" N   GLU A 440 "
            pdb=" OE1 GLU A 440 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" NZ  LYS A 358 "
            pdb=" O   LYS A 551 "
     model   vdw
     2.297 3.120
  ... (remaining 68993 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.570
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
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   0.160   8936  Z= 0.325
  Angle     :  0.926  18.185  12094  Z= 0.526
  Chirality :  0.049   0.609   1464
  Planarity :  0.007   0.149   1518
  Dihedral  : 16.160  86.253   3304
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.96 %
    Allowed  :  6.23 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 25.73 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1140
  helix:  1.56 (0.19), residues: 750
  sheet:  0.96 (0.65), residues: 70
  loop : -3.85 (0.28), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP B 413 
 HIS   0.003   0.001   HIS B 141 
 PHE   0.020   0.001   PHE A 348 
 TYR   0.024   0.002   TYR B 408 
 ARG   0.007   0.001   ARG A 414 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  259 MET cc_start: 0.8502 (tpt) cc_final: 0.8168 (tpt)
REVERT: B  439 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6999 (tt)
  outliers start: 10
  outliers final: 4
  residues processed: 137
  average time/residue: 0.1956
  time to fit residues: 38.1987
Evaluate side-chains
  132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  439 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 89 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 54 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 141 HIS
B 141 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.205645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.138621 restraints weight = 12724.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.139334 restraints weight = 7351.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.141992 restraints weight = 4438.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.0932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8936  Z= 0.208
  Angle     :  0.705  13.024  12094  Z= 0.358
  Chirality :  0.043   0.220   1464
  Planarity :  0.005   0.079   1518
  Dihedral  :  6.084  59.892   1232
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  6.84 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 23.03 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.26), residues: 1140
  helix:  2.09 (0.19), residues: 760
  sheet:  0.85 (0.64), residues: 70
  loop : -3.88 (0.28), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 413 
 HIS   0.003   0.001   HIS B 141 
 PHE   0.014   0.001   PHE B 390 
 TYR   0.029   0.002   TYR B 408 
 ARG   0.004   0.000   ARG A 414 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 128
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8151 (ttpp) cc_final: 0.7805 (ttpp)
REVERT: A  368 LYS cc_start: 0.6485 (tptp) cc_final: 0.6205 (tptp)
REVERT: A  580 MET cc_start: 0.4747 (mpp) cc_final: 0.3888 (mpp)
REVERT: B   61 ASN cc_start: 0.4500 (OUTLIER) cc_final: 0.4104 (t0)
REVERT: B  109 LYS cc_start: 0.8199 (tmmt) cc_final: 0.7969 (tmmt)
REVERT: B  439 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7051 (tt)
  outliers start: 34
  outliers final: 18
  residues processed: 153
  average time/residue: 0.1835
  time to fit residues: 40.5834
Evaluate side-chains
  144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  559 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 101 optimal weight:    0.5980
   chunk 33 optimal weight:    8.9990
   chunk 16 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.206224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.135493 restraints weight = 13012.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.139875 restraints weight = 6421.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.142766 restraints weight = 4182.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8936  Z= 0.192
  Angle     :  0.666  12.499  12094  Z= 0.335
  Chirality :  0.042   0.223   1464
  Planarity :  0.005   0.083   1518
  Dihedral  :  5.826  57.458   1230
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.84 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 22.61 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 1140
  helix:  2.25 (0.19), residues: 760
  sheet:  0.71 (0.63), residues: 70
  loop : -3.76 (0.30), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP A 413 
 HIS   0.003   0.001   HIS B 560 
 PHE   0.007   0.001   PHE A 303 
 TYR   0.025   0.002   TYR B 408 
 ARG   0.003   0.000   ARG A 126 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 130
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7600 (tptt)
REVERT: A  169 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8871 (mm)
REVERT: A  335 GLU cc_start: 0.7855 (pm20) cc_final: 0.7619 (pm20)
REVERT: A  368 LYS cc_start: 0.6668 (tptp) cc_final: 0.6372 (tptp)
REVERT: A  385 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8464 (mtmm)
REVERT: A  483 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.6261 (mp10)
REVERT: B   61 ASN cc_start: 0.4343 (OUTLIER) cc_final: 0.3944 (t0)
REVERT: B  126 ARG cc_start: 0.7224 (mtp180) cc_final: 0.6857 (mtm110)
REVERT: B  160 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7960 (m-80)
REVERT: B  225 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8262 (mm-30)
REVERT: B  259 MET cc_start: 0.8636 (tpp) cc_final: 0.8215 (tpp)
REVERT: B  294 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6785 (mm)
REVERT: B  439 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7049 (tp)
  outliers start: 47
  outliers final: 27
  residues processed: 166
  average time/residue: 0.1818
  time to fit residues: 43.9403
Evaluate side-chains
  158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  483 GLN
Chi-restraints excluded: chain A residue  485 GLN
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  559 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 104 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.7584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.201957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.129788 restraints weight = 12963.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.134005 restraints weight = 6657.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.136766 restraints weight = 4437.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8936  Z= 0.269
  Angle     :  0.704   9.935  12094  Z= 0.355
  Chirality :  0.043   0.240   1464
  Planarity :  0.005   0.087   1518
  Dihedral  :  5.751  54.602   1230
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.32 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 23.86 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 1140
  helix:  2.24 (0.19), residues: 756
  sheet:  0.71 (0.63), residues: 70
  loop : -3.66 (0.30), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 413 
 HIS   0.003   0.001   HIS B 560 
 PHE   0.013   0.001   PHE A 390 
 TYR   0.026   0.002   TYR A 114 
 ARG   0.002   0.000   ARG B 571 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 128
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7673 (tptt)
REVERT: A  130 ASP cc_start: 0.7659 (m-30) cc_final: 0.7373 (m-30)
REVERT: A  169 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8911 (mm)
REVERT: A  271 MET cc_start: 0.8482 (mmt) cc_final: 0.8121 (mmm)
REVERT: A  368 LYS cc_start: 0.6806 (tptp) cc_final: 0.6501 (tptp)
REVERT: A  385 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8509 (mtmm)
REVERT: A  411 GLU cc_start: 0.9321 (tm-30) cc_final: 0.9105 (tm-30)
REVERT: A  428 SER cc_start: 0.8582 (t) cc_final: 0.7641 (p)
REVERT: B   61 ASN cc_start: 0.4217 (OUTLIER) cc_final: 0.3811 (t0)
REVERT: B  126 ARG cc_start: 0.7229 (mtp180) cc_final: 0.6860 (mtm110)
REVERT: B  160 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7873 (m-80)
REVERT: B  225 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8409 (mm-30)
REVERT: B  259 MET cc_start: 0.8705 (tpp) cc_final: 0.8316 (tpp)
REVERT: B  294 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.6907 (mm)
REVERT: B  295 MET cc_start: 0.7074 (mtp) cc_final: 0.6846 (mtt)
REVERT: B  439 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7012 (tp)
REVERT: B  501 MET cc_start: 0.8372 (tmm) cc_final: 0.8093 (tmm)
  outliers start: 57
  outliers final: 36
  residues processed: 172
  average time/residue: 0.1762
  time to fit residues: 44.5629
Evaluate side-chains
  162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 121
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  559 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 107 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   chunk 106 optimal weight:   30.0000
   chunk 54 optimal weight:    0.9980
   chunk 88 optimal weight:    6.9990
   chunk 82 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0020
   chunk 23 optimal weight:    0.6980
   overall best weight:    1.3392

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

Flipped N/Q/H residues before XYZ refinement:
A 496 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.205464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.139954 restraints weight = 12844.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.141096 restraints weight = 7201.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.143540 restraints weight = 4377.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   8936  Z= 0.226
  Angle     :  0.689  14.396  12094  Z= 0.343
  Chirality :  0.042   0.227   1464
  Planarity :  0.005   0.086   1518
  Dihedral  :  5.673  52.827   1230
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.49 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 25.31 %
    Favored  : 68.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.26), residues: 1140
  helix:  2.33 (0.19), residues: 758
  sheet:  0.81 (0.64), residues: 70
  loop : -3.64 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 413 
 HIS   0.003   0.001   HIS B 560 
 PHE   0.009   0.001   PHE A 160 
 TYR   0.022   0.001   TYR B 114 
 ARG   0.002   0.000   ARG B 571 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 128
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7668 (tptt)
REVERT: A  130 ASP cc_start: 0.7663 (m-30) cc_final: 0.7276 (m-30)
REVERT: A  169 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8911 (mm)
REVERT: A  271 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8101 (mmm)
REVERT: A  368 LYS cc_start: 0.6829 (tptp) cc_final: 0.6480 (tptp)
REVERT: A  385 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8491 (mtmm)
REVERT: A  428 SER cc_start: 0.8603 (t) cc_final: 0.7754 (p)
REVERT: B   61 ASN cc_start: 0.4454 (OUTLIER) cc_final: 0.3935 (t0)
REVERT: B  109 LYS cc_start: 0.8340 (tmmt) cc_final: 0.8102 (tmmt)
REVERT: B  126 ARG cc_start: 0.7205 (mtp180) cc_final: 0.6865 (mtm110)
REVERT: B  160 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7902 (m-80)
REVERT: B  225 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8435 (mm-30)
REVERT: B  259 MET cc_start: 0.8614 (tpp) cc_final: 0.8281 (tpp)
REVERT: B  294 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.6764 (mm)
REVERT: B  439 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7059 (tp)
  outliers start: 55
  outliers final: 38
  residues processed: 166
  average time/residue: 0.1744
  time to fit residues: 42.7552
Evaluate side-chains
  169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 124
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  559 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:   20.0000
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 102 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 93 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9990
   chunk 90 optimal weight:    8.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 485 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 = 0.4631 r_free = 0.4631 target = 0.206877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.140389 restraints weight = 12667.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.143234 restraints weight = 6817.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.145295 restraints weight = 3944.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8936  Z= 0.195
  Angle     :  0.675  11.663  12094  Z= 0.335
  Chirality :  0.041   0.222   1464
  Planarity :  0.005   0.085   1518
  Dihedral  :  5.576  50.971   1229
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.67 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 25.83 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.26), residues: 1140
  helix:  2.39 (0.19), residues: 752
  sheet:  0.98 (0.65), residues: 70
  loop : -3.61 (0.30), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 413 
 HIS   0.003   0.001   HIS B 560 
 PHE   0.016   0.001   PHE A  57 
 TYR   0.022   0.001   TYR B 114 
 ARG   0.002   0.000   ARG A 389 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 127
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7635 (tptt)
REVERT: A  156 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8419 (mt)
REVERT: A  169 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8813 (mm)
REVERT: A  271 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8068 (mmm)
REVERT: A  390 PHE cc_start: 0.8496 (m-10) cc_final: 0.8233 (m-10)
REVERT: A  428 SER cc_start: 0.8638 (t) cc_final: 0.7859 (p)
REVERT: B   61 ASN cc_start: 0.4417 (OUTLIER) cc_final: 0.3920 (t0)
REVERT: B  126 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6605 (mtm110)
REVERT: B  160 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7937 (m-80)
REVERT: B  249 LEU cc_start: 0.8271 (tt) cc_final: 0.7283 (mp)
REVERT: B  259 MET cc_start: 0.8581 (tpp) cc_final: 0.8259 (tpp)
REVERT: B  294 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6462 (mm)
REVERT: B  439 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7064 (tp)
REVERT: B  501 MET cc_start: 0.8330 (tmm) cc_final: 0.8121 (tmm)
  outliers start: 55
  outliers final: 34
  residues processed: 169
  average time/residue: 0.1786
  time to fit residues: 44.2755
Evaluate side-chains
  167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 124
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  559 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 55 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 79 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 98 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 93 optimal weight:   20.0000
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.203745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.137237 restraints weight = 12895.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.138615 restraints weight = 6983.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.141568 restraints weight = 4336.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8936  Z= 0.272
  Angle     :  0.726  13.814  12094  Z= 0.360
  Chirality :  0.043   0.226   1464
  Planarity :  0.005   0.084   1518
  Dihedral  :  5.600  46.253   1229
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  6.40 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 25.41 %
    Favored  : 67.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.26), residues: 1140
  helix:  2.23 (0.19), residues: 756
  sheet:  0.96 (0.65), residues: 70
  loop : -3.60 (0.30), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 164 
 HIS   0.003   0.001   HIS A 535 
 PHE   0.020   0.001   PHE A 348 
 TYR   0.020   0.001   TYR B 114 
 ARG   0.002   0.000   ARG B 571 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 127
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7738 (tptt)
REVERT: A  122 GLU cc_start: 0.7922 (tp30) cc_final: 0.7574 (tm-30)
REVERT: A  169 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8863 (mm)
REVERT: A  271 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8094 (mmm)
REVERT: A  428 SER cc_start: 0.8696 (t) cc_final: 0.8066 (p)
REVERT: B   61 ASN cc_start: 0.4370 (OUTLIER) cc_final: 0.3874 (t0)
REVERT: B  126 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6649 (mtm110)
REVERT: B  160 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8026 (m-80)
REVERT: B  225 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8523 (mm-30)
REVERT: B  249 LEU cc_start: 0.8431 (tt) cc_final: 0.7333 (mp)
REVERT: B  259 MET cc_start: 0.8638 (tpp) cc_final: 0.8189 (tpp)
REVERT: B  290 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6943 (mp)
REVERT: B  294 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6584 (mm)
REVERT: B  436 CYS cc_start: 0.7819 (t) cc_final: 0.6729 (p)
REVERT: B  439 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6915 (tp)
REVERT: B  494 LEU cc_start: 0.7998 (mt) cc_final: 0.7772 (tt)
REVERT: B  501 MET cc_start: 0.8373 (tmm) cc_final: 0.8149 (tmm)
  outliers start: 65
  outliers final: 46
  residues processed: 174
  average time/residue: 0.1672
  time to fit residues: 43.2956
Evaluate side-chains
  179 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 124
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  197 ASP
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  294 ILE
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  559 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 49 optimal weight:   20.0000
   chunk 2 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 90 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 34 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 101 optimal weight:    8.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.207033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.141870 restraints weight = 12896.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.142957 restraints weight = 7072.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.146093 restraints weight = 4224.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8936  Z= 0.189
  Angle     :  0.703  13.945  12094  Z= 0.345
  Chirality :  0.042   0.231   1464
  Planarity :  0.005   0.084   1518
  Dihedral  :  5.514  46.234   1229
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.58 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 27.39 %
    Favored  : 67.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1140
  helix:  2.26 (0.19), residues: 760
  sheet:  1.18 (0.66), residues: 70
  loop : -3.60 (0.30), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 413 
 HIS   0.003   0.001   HIS B 560 
 PHE   0.021   0.001   PHE A 348 
 TYR   0.021   0.001   TYR B 114 
 ARG   0.002   0.000   ARG B 495 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 136
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7635 (tptt)
REVERT: A  169 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8791 (mm)
REVERT: A  271 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8013 (mmm)
REVERT: A  428 SER cc_start: 0.8620 (t) cc_final: 0.7959 (p)
REVERT: B   61 ASN cc_start: 0.4479 (OUTLIER) cc_final: 0.3947 (t0)
REVERT: B  126 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6465 (mtm110)
REVERT: B  130 ASP cc_start: 0.7487 (m-30) cc_final: 0.7050 (m-30)
REVERT: B  160 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8028 (m-80)
REVERT: B  249 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7289 (mp)
REVERT: B  259 MET cc_start: 0.8541 (tpp) cc_final: 0.8189 (tpp)
REVERT: B  501 MET cc_start: 0.8396 (tmm) cc_final: 0.8174 (tmm)
  outliers start: 50
  outliers final: 33
  residues processed: 171
  average time/residue: 0.1597
  time to fit residues: 40.6017
Evaluate side-chains
  172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 132
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  559 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 113 optimal weight:   20.0000
   chunk 111 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 108 optimal weight:   30.0000
   chunk 96 optimal weight:    5.9990
   chunk 73 optimal weight:    0.5980
   chunk 84 optimal weight:    0.5980
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** 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 = 0.4619 r_free = 0.4619 target = 0.205094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.142711 restraints weight = 13836.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.144462 restraints weight = 7258.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.144719 restraints weight = 4805.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8936  Z= 0.265
  Angle     :  0.758  13.996  12094  Z= 0.373
  Chirality :  0.044   0.291   1464
  Planarity :  0.005   0.083   1518
  Dihedral  :  5.431  46.709   1227
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.32 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 27.59 %
    Favored  : 66.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1140
  helix:  2.14 (0.19), residues: 758
  sheet:  1.08 (0.65), residues: 70
  loop : -3.55 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 413 
 HIS   0.003   0.001   HIS B 560 
 PHE   0.019   0.001   PHE A 348 
 TYR   0.019   0.001   TYR B 114 
 ARG   0.004   0.000   ARG A 484 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 130
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7790 (tptt)
REVERT: A  122 GLU cc_start: 0.7849 (tp30) cc_final: 0.7527 (tm-30)
REVERT: A  169 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8882 (mm)
REVERT: A  271 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8006 (mmm)
REVERT: A  388 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7917 (mm-30)
REVERT: A  428 SER cc_start: 0.8642 (t) cc_final: 0.8018 (p)
REVERT: B   61 ASN cc_start: 0.4610 (OUTLIER) cc_final: 0.4058 (t0)
REVERT: B  126 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6647 (mtm110)
REVERT: B  160 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8030 (m-80)
REVERT: B  249 LEU cc_start: 0.8327 (tt) cc_final: 0.7344 (mp)
REVERT: B  259 MET cc_start: 0.8684 (tpp) cc_final: 0.8325 (tpp)
REVERT: B  436 CYS cc_start: 0.7803 (t) cc_final: 0.6647 (p)
REVERT: B  439 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.6936 (tp)
  outliers start: 53
  outliers final: 40
  residues processed: 167
  average time/residue: 0.1691
  time to fit residues: 41.9439
Evaluate side-chains
  173 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 126
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  561 HIS
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  197 ASP
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  559 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 99 optimal weight:    7.9990
   chunk 84 optimal weight:    0.5980
   chunk 43 optimal weight:    0.1980
   chunk 102 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 113 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.207486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.143002 restraints weight = 13723.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.144129 restraints weight = 7527.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.145533 restraints weight = 4530.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8936  Z= 0.201
  Angle     :  0.745  14.226  12094  Z= 0.365
  Chirality :  0.043   0.306   1464
  Planarity :  0.005   0.082   1518
  Dihedral  :  5.386  46.714   1227
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.67 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 28.53 %
    Favored  : 67.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1140
  helix:  2.20 (0.19), residues: 754
  sheet:  1.18 (0.65), residues: 70
  loop : -3.51 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 104 
 HIS   0.003   0.001   HIS B 560 
 PHE   0.019   0.001   PHE A 348 
 TYR   0.021   0.001   TYR B 114 
 ARG   0.004   0.000   ARG B 100 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 130
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7651 (tptt)
REVERT: A  122 GLU cc_start: 0.7791 (tp30) cc_final: 0.7499 (tm-30)
REVERT: A  169 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8773 (mm)
REVERT: A  271 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7947 (mmm)
REVERT: A  324 GLU cc_start: 0.7996 (pm20) cc_final: 0.7580 (mp0)
REVERT: A  411 GLU cc_start: 0.9368 (tm-30) cc_final: 0.9120 (tm-30)
REVERT: A  428 SER cc_start: 0.8663 (t) cc_final: 0.8063 (p)
REVERT: B   61 ASN cc_start: 0.4646 (OUTLIER) cc_final: 0.4115 (t0)
REVERT: B  126 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6724 (mtm110)
REVERT: B  160 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7989 (m-80)
REVERT: B  249 LEU cc_start: 0.8292 (tt) cc_final: 0.7278 (mp)
REVERT: B  436 CYS cc_start: 0.7777 (t) cc_final: 0.6625 (p)
REVERT: B  454 MET cc_start: 0.6488 (mmp) cc_final: 0.5489 (ptm)
REVERT: B  501 MET cc_start: 0.8281 (tmm) cc_final: 0.8012 (tmm)
  outliers start: 42
  outliers final: 34
  residues processed: 158
  average time/residue: 0.1726
  time to fit residues: 40.3661
Evaluate side-chains
  167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  109 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  561 HIS
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  304 PHE
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  559 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0770
   chunk 102 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 94 optimal weight:    6.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    0.6742

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
** A 485 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 = 0.4645 r_free = 0.4645 target = 0.207996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.143409 restraints weight = 13804.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.144316 restraints weight = 7715.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.145785 restraints weight = 4669.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8936  Z= 0.208
  Angle     :  0.768  13.663  12094  Z= 0.373
  Chirality :  0.043   0.313   1464
  Planarity :  0.005   0.079   1518
  Dihedral  :  5.390  46.973   1227
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.58 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 28.73 %
    Favored  : 66.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.26), residues: 1140
  helix:  2.24 (0.19), residues: 748
  sheet:  1.14 (0.65), residues: 70
  loop : -3.46 (0.30), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 413 
 HIS   0.003   0.001   HIS B 560 
 PHE   0.018   0.001   PHE A 348 
 TYR   0.025   0.001   TYR B 114 
 ARG   0.003   0.000   ARG B 100 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2734.20 seconds
wall clock time: 49 minutes 49.16 seconds (2989.16 seconds total)