Starting phenix.real_space_refine
on Wed Sep 17 12:49:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rga_19131/09_2025/8rga_19131.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rga_19131/09_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_19131/09_2025/8rga_19131.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rga_19131/09_2025/8rga_19131.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rga_19131/09_2025/8rga_19131.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rga_19131/09_2025/8rga_19131.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.27, per 1000 atoms: 0.26
  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: 0.80
  Conformation dependent library (CDL) restraints added in 337.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.21
  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: 1.18

  Time building geometry restraints manager: 1.04 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: 0.02
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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.360
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.060
-------------------------------------------------------------------------------
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= 0.250
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (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
 ARG   0.007   0.001   ARG A 414 
 TYR   0.024   0.002   TYR B 408 
 PHE   0.020   0.001   PHE A 348 
 TRP   0.045   0.003   TRP B 413 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 8936)
  covalent geometry    : angle       0.92627 (12094)
  hydrogen bonds       : bond        0.13894 (  592)
  hydrogen bonds       : angle       6.11017 ( 1752)

*********************** 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  : 0.320 
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: 0.0789
  time to fit residues: 15.8316
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  : 0.344 
-------------------------------------------------------------------------------
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 108 optimal weight:   30.0000
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0980
   chunk 100 optimal weight:    0.8980
   overall best weight:    2.1784

-------------------------------------------------------------------------------
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 = 0.4578 r_free = 0.4578 target = 0.202051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.130682 restraints weight = 12872.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.134831 restraints weight = 6637.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.137424 restraints weight = 4408.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.138778 restraints weight = 3483.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.139934 restraints weight = 3072.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   8936  Z= 0.226
  Angle     :  0.749  12.939  12094  Z= 0.382
  Chirality :  0.044   0.228   1464
  Planarity :  0.005   0.078   1518
  Dihedral  :  6.109  57.564   1232
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  6.49 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 22.30 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.26), residues: 1140
  helix:  2.03 (0.19), residues: 758
  sheet:  0.78 (0.64), residues: 70
  loop : -3.88 (0.28), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 126 
 TYR   0.027   0.002   TYR B 408 
 PHE   0.013   0.001   PHE B 390 
 TRP   0.019   0.002   TRP A 413 
 HIS   0.006   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 8936)
  covalent geometry    : angle       0.74948 (12094)
  hydrogen bonds       : bond        0.05379 (  592)
  hydrogen bonds       : angle       4.77527 ( 1752)

*********************** 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
  178 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 131
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 LYS cc_start: 0.6806 (tptp) cc_final: 0.6467 (tptp)
REVERT: A  390 PHE cc_start: 0.8485 (m-10) cc_final: 0.8283 (m-10)
REVERT: A  483 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.6226 (mp10)
REVERT: A  580 MET cc_start: 0.4708 (mpp) cc_final: 0.3818 (mpp)
REVERT: B   61 ASN cc_start: 0.3991 (OUTLIER) cc_final: 0.3711 (t0)
REVERT: B  109 LYS cc_start: 0.8241 (tmmt) cc_final: 0.8010 (tmmt)
REVERT: B  294 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.6962 (mm)
REVERT: B  439 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6960 (tt)
REVERT: B  501 MET cc_start: 0.8203 (tmm) cc_final: 0.7951 (tmm)
  outliers start: 47
  outliers final: 26
  residues processed: 163
  average time/residue: 0.0784
  time to fit residues: 18.8369
Evaluate side-chains
  152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 122
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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  149 ILE
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  203 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 A residue  483 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   67 ILE
Chi-restraints excluded: chain B residue  157 THR
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  224 VAL
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  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 84 optimal weight:    0.8980
   chunk 58 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 106 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.4594 r_free = 0.4594 target = 0.204065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.133539 restraints weight = 12887.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.137926 restraints weight = 6417.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.140627 restraints weight = 4193.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.142015 restraints weight = 3301.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.143188 restraints weight = 2915.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8936  Z= 0.151
  Angle     :  0.693  12.987  12094  Z= 0.346
  Chirality :  0.042   0.227   1464
  Planarity :  0.005   0.084   1518
  Dihedral  :  5.932  56.402   1232
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  7.11 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 24.17 %
    Favored  : 70.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.26), residues: 1140
  helix:  2.19 (0.19), residues: 760
  sheet:  0.74 (0.64), residues: 70
  loop : -3.77 (0.29), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 414 
 TYR   0.026   0.002   TYR B 408 
 PHE   0.008   0.001   PHE A 303 
 TRP   0.016   0.002   TRP A 413 
 HIS   0.002   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8936)
  covalent geometry    : angle       0.69333 (12094)
  hydrogen bonds       : bond        0.04735 (  592)
  hydrogen bonds       : angle       4.39275 ( 1752)

*********************** 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
  180 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 130
  time to evaluate  : 0.322 
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: 0.8103 (ttpp) cc_final: 0.7559 (tptt)
REVERT: A  368 LYS cc_start: 0.6785 (tptp) cc_final: 0.6460 (tptp)
REVERT: A  385 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8485 (mtmm)
REVERT: A  411 GLU cc_start: 0.9348 (tm-30) cc_final: 0.9067 (tm-30)
REVERT: A  483 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6290 (mp10)
REVERT: B   29 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7847 (mp)
REVERT: B   61 ASN cc_start: 0.4013 (OUTLIER) cc_final: 0.3679 (t0)
REVERT: B  160 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7913 (m-80)
REVERT: B  165 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6873 (ptpt)
REVERT: B  259 MET cc_start: 0.8618 (tpp) cc_final: 0.8177 (tpp)
REVERT: B  294 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6843 (mm)
REVERT: B  439 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6949 (tp)
REVERT: B  501 MET cc_start: 0.8348 (tmm) cc_final: 0.7896 (tmm)
  outliers start: 50
  outliers final: 23
  residues processed: 170
  average time/residue: 0.0791
  time to fit residues: 19.8764
Evaluate side-chains
  155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  304 PHE
Chi-restraints excluded: chain A residue  409 SER
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 A residue  501 MET
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  165 LYS
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  212 GLU
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  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 29 optimal weight:    1.9990
   chunk 109 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 100 optimal weight:   30.0000
   chunk 26 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0770
   chunk 61 optimal weight:    0.9990
   chunk 105 optimal weight:    9.9990
   chunk 111 optimal weight:   30.0000
   chunk 54 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    1.0144

-------------------------------------------------------------------------------
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 = 0.4588 r_free = 0.4588 target = 0.203560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.132726 restraints weight = 12970.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.137118 restraints weight = 6506.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.139846 restraints weight = 4255.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.141626 restraints weight = 3333.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.142296 restraints weight = 2905.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8936  Z= 0.147
  Angle     :  0.680  12.686  12094  Z= 0.341
  Chirality :  0.043   0.252   1464
  Planarity :  0.005   0.089   1518
  Dihedral  :  5.750  54.368   1229
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.67 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 23.65 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.26), residues: 1140
  helix:  2.25 (0.19), residues: 760
  sheet:  0.78 (0.64), residues: 70
  loop : -3.77 (0.30), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 414 
 TYR   0.027   0.002   TYR A 114 
 PHE   0.011   0.001   PHE A 160 
 TRP   0.016   0.002   TRP A 413 
 HIS   0.002   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8936)
  covalent geometry    : angle       0.68021 (12094)
  hydrogen bonds       : bond        0.04431 (  592)
  hydrogen bonds       : angle       4.25041 ( 1752)

*********************** 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
  190 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 128
  time to evaluate  : 0.360 
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: 0.8114 (ttpp) cc_final: 0.7624 (tptt)
REVERT: A  130 ASP cc_start: 0.7587 (m-30) cc_final: 0.7287 (m-30)
REVERT: A  169 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8835 (mm)
REVERT: A  271 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8085 (mmm)
REVERT: A  385 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8521 (mtmm)
REVERT: A  411 GLU cc_start: 0.9312 (tm-30) cc_final: 0.9050 (tm-30)
REVERT: B   29 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7778 (mp)
REVERT: B   61 ASN cc_start: 0.4124 (OUTLIER) cc_final: 0.3741 (t0)
REVERT: B  126 ARG cc_start: 0.7206 (mtp180) cc_final: 0.6858 (mtm110)
REVERT: B  160 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7866 (m-80)
REVERT: B  259 MET cc_start: 0.8639 (tpp) cc_final: 0.8292 (tpp)
REVERT: B  294 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.6728 (mm)
REVERT: B  439 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6961 (tp)
REVERT: B  501 MET cc_start: 0.8382 (tmm) cc_final: 0.7855 (tmm)
  outliers start: 62
  outliers final: 40
  residues processed: 177
  average time/residue: 0.0749
  time to fit residues: 19.7080
Evaluate side-chains
  170 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 123
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
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  125 SER
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 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  256 LEU
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  304 PHE
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain B residue   29 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  134 VAL
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  212 GLU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  257 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:   10.0000
   chunk 72 optimal weight:    0.0980
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 109 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 21 optimal weight:    0.4980
   chunk 60 optimal weight:    0.6980
   chunk 37 optimal weight:    7.9990
   chunk 43 optimal weight:    0.5980
   chunk 44 optimal weight:    8.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4638 r_free = 0.4638 target = 0.207932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.139138 restraints weight = 12852.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.143960 restraints weight = 6072.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.146978 restraints weight = 3849.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.148614 restraints weight = 2972.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.149513 restraints weight = 2591.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   8936  Z= 0.137
  Angle     :  0.674  11.070  12094  Z= 0.335
  Chirality :  0.042   0.229   1464
  Planarity :  0.005   0.088   1518
  Dihedral  :  5.669  53.751   1229
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.75 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 25.10 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.26), residues: 1140
  helix:  2.33 (0.19), residues: 754
  sheet:  0.98 (0.65), residues: 70
  loop : -3.64 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 414 
 TYR   0.023   0.002   TYR A 114 
 PHE   0.013   0.001   PHE B 286 
 TRP   0.015   0.001   TRP A 413 
 HIS   0.003   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8936)
  covalent geometry    : angle       0.67356 (12094)
  hydrogen bonds       : bond        0.04255 (  592)
  hydrogen bonds       : angle       4.14980 ( 1752)

*********************** 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
  179 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 128
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8061 (ttpp) cc_final: 0.7642 (tptt)
REVERT: A  130 ASP cc_start: 0.7462 (m-30) cc_final: 0.7185 (m-30)
REVERT: A  169 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8825 (mm)
REVERT: A  271 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7989 (mmm)
REVERT: A  428 SER cc_start: 0.8470 (t) cc_final: 0.7601 (p)
REVERT: A  501 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8299 (tmm)
REVERT: B   29 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7622 (mp)
REVERT: B   61 ASN cc_start: 0.3977 (OUTLIER) cc_final: 0.3711 (t0)
REVERT: B  126 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6656 (mtm110)
REVERT: B  160 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7866 (m-80)
REVERT: B  249 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7297 (mp)
REVERT: B  259 MET cc_start: 0.8657 (tpp) cc_final: 0.8334 (tpp)
REVERT: B  439 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6947 (tp)
  outliers start: 51
  outliers final: 31
  residues processed: 165
  average time/residue: 0.0739
  time to fit residues: 18.4004
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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  125 SER
Chi-restraints excluded: chain A residue  147 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  212 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  256 LEU
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  409 SER
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  561 HIS
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   40 THR
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  279 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 93 optimal weight:    8.9990
   chunk 51 optimal weight:   30.0000
   chunk 86 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 109 optimal weight:   10.0000
   chunk 95 optimal weight:    8.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.4620 r_free = 0.4620 target = 0.205304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.139076 restraints weight = 12960.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.140997 restraints weight = 6891.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.144271 restraints weight = 4152.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.145297 restraints weight = 3150.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.144960 restraints weight = 2956.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8936  Z= 0.181
  Angle     :  0.707  10.296  12094  Z= 0.353
  Chirality :  0.042   0.229   1464
  Planarity :  0.005   0.087   1518
  Dihedral  :  5.633  50.586   1229
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  5.96 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 25.41 %
    Favored  : 68.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.26), residues: 1140
  helix:  2.26 (0.19), residues: 754
  sheet:  0.89 (0.64), residues: 70
  loop : -3.59 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 571 
 TYR   0.020   0.001   TYR B 114 
 PHE   0.017   0.001   PHE A 348 
 TRP   0.010   0.001   TRP A 413 
 HIS   0.005   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 8936)
  covalent geometry    : angle       0.70708 (12094)
  hydrogen bonds       : bond        0.04494 (  592)
  hydrogen bonds       : angle       4.29828 ( 1752)

*********************** 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
  189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 126
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7644 (tptt)
REVERT: A  130 ASP cc_start: 0.7660 (m-30) cc_final: 0.7316 (m-30)
REVERT: A  169 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8854 (mm)
REVERT: A  271 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8106 (mmm)
REVERT: A  411 GLU cc_start: 0.9328 (tm-30) cc_final: 0.9088 (tm-30)
REVERT: A  428 SER cc_start: 0.8528 (t) cc_final: 0.7678 (p)
REVERT: A  501 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8280 (tmm)
REVERT: B   29 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7859 (mp)
REVERT: B   61 ASN cc_start: 0.4280 (OUTLIER) cc_final: 0.3841 (t0)
REVERT: B  109 LYS cc_start: 0.8347 (tmmt) cc_final: 0.8135 (tmmt)
REVERT: B  126 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6821 (mtm110)
REVERT: B  160 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7914 (m-80)
REVERT: B  249 LEU cc_start: 0.8415 (tt) cc_final: 0.7302 (mp)
REVERT: B  259 MET cc_start: 0.8651 (tpp) cc_final: 0.8227 (tpp)
REVERT: B  294 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.6774 (mm)
REVERT: B  436 CYS cc_start: 0.7780 (t) cc_final: 0.6745 (p)
REVERT: B  439 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6963 (tp)
REVERT: B  501 MET cc_start: 0.8312 (tmm) cc_final: 0.7834 (tmm)
  outliers start: 63
  outliers final: 45
  residues processed: 171
  average time/residue: 0.0790
  time to fit residues: 20.2319
Evaluate side-chains
  174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 119
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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  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  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  409 SER
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  501 MET
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   29 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  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  212 GLU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  257 VAL
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  448 ILE
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 88 optimal weight:    2.9990
   chunk 106 optimal weight:   30.0000
   chunk 18 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0870
   chunk 58 optimal weight:    0.0970
   chunk 5 optimal weight:    6.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.8362

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.203577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.135799 restraints weight = 12991.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.138789 restraints weight = 6895.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.141629 restraints weight = 4336.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.142389 restraints weight = 3307.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.142314 restraints weight = 3307.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8936  Z= 0.185
  Angle     :  0.728   9.936  12094  Z= 0.362
  Chirality :  0.043   0.229   1464
  Planarity :  0.005   0.086   1518
  Dihedral  :  5.600  45.833   1229
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.23 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 25.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.26), residues: 1140
  helix:  2.22 (0.19), residues: 752
  sheet:  1.03 (0.64), residues: 70
  loop : -3.53 (0.30), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 389 
 TYR   0.020   0.001   TYR A 114 
 PHE   0.019   0.001   PHE A 348 
 TRP   0.008   0.001   TRP B 164 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 8936)
  covalent geometry    : angle       0.72816 (12094)
  hydrogen bonds       : bond        0.04565 (  592)
  hydrogen bonds       : angle       4.31185 ( 1752)

*********************** 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
  193 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 127
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7715 (tptt)
REVERT: A  122 GLU cc_start: 0.7915 (tp30) cc_final: 0.7538 (tm-30)
REVERT: A  130 ASP cc_start: 0.7745 (m-30) cc_final: 0.7394 (m-30)
REVERT: A  169 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8778 (mm)
REVERT: A  271 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8073 (mmm)
REVERT: A  428 SER cc_start: 0.8609 (t) cc_final: 0.7880 (p)
REVERT: A  454 MET cc_start: 0.8213 (mmm) cc_final: 0.7991 (mmp)
REVERT: B   29 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7739 (mp)
REVERT: B   61 ASN cc_start: 0.4258 (OUTLIER) cc_final: 0.3782 (t0)
REVERT: B  126 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6648 (mtm110)
REVERT: B  160 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7892 (m-80)
REVERT: B  249 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7322 (mp)
REVERT: B  259 MET cc_start: 0.8608 (tpp) cc_final: 0.8170 (tpp)
REVERT: B  294 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.6848 (mm)
REVERT: B  436 CYS cc_start: 0.7758 (t) cc_final: 0.6714 (p)
REVERT: B  439 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6890 (tp)
REVERT: B  494 LEU cc_start: 0.7999 (mt) cc_final: 0.7783 (tt)
REVERT: B  501 MET cc_start: 0.8219 (tmm) cc_final: 0.7652 (tmm)
  outliers start: 66
  outliers final: 49
  residues processed: 174
  average time/residue: 0.0776
  time to fit residues: 20.2200
Evaluate side-chains
  180 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 121
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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   74 PHE
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  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  409 SER
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  501 MET
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   29 LEU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   40 THR
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  199 THR
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  294 ILE
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  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 68 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 108 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 113 optimal weight:    9.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
B 208 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.208187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.146890 restraints weight = 12814.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.145960 restraints weight = 6204.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.147139 restraints weight = 4097.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.147744 restraints weight = 3734.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.147847 restraints weight = 3425.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8936  Z= 0.141
  Angle     :  0.712  16.063  12094  Z= 0.348
  Chirality :  0.042   0.229   1464
  Planarity :  0.005   0.085   1518
  Dihedral  :  5.508  45.969   1229
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  6.32 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 27.59 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.26), residues: 1140
  helix:  2.24 (0.19), residues: 756
  sheet:  1.24 (0.65), residues: 70
  loop : -3.57 (0.30), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 389 
 TYR   0.022   0.001   TYR B 114 
 PHE   0.020   0.001   PHE A 348 
 TRP   0.008   0.001   TRP B 164 
 HIS   0.003   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8936)
  covalent geometry    : angle       0.71157 (12094)
  hydrogen bonds       : bond        0.04283 (  592)
  hydrogen bonds       : angle       4.16931 ( 1752)

*********************** 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
  184 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 132
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7532 (tptp)
REVERT: A  169 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8743 (mm)
REVERT: A  271 MET cc_start: 0.8374 (mmt) cc_final: 0.8141 (mmm)
REVERT: A  317 MET cc_start: 0.8598 (tpp) cc_final: 0.8265 (mmt)
REVERT: A  411 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9035 (tm-30)
REVERT: A  428 SER cc_start: 0.8533 (t) cc_final: 0.7860 (p)
REVERT: B   29 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7698 (mp)
REVERT: B   61 ASN cc_start: 0.4438 (OUTLIER) cc_final: 0.3959 (t0)
REVERT: B  126 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6654 (mtm110)
REVERT: B  160 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7936 (m-80)
REVERT: B  249 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7283 (mp)
REVERT: B  259 MET cc_start: 0.8607 (tpp) cc_final: 0.8264 (tpp)
REVERT: B  436 CYS cc_start: 0.7712 (t) cc_final: 0.6504 (p)
REVERT: B  494 LEU cc_start: 0.7857 (mt) cc_final: 0.7646 (tt)
REVERT: B  501 MET cc_start: 0.8348 (tmm) cc_final: 0.7860 (tmm)
  outliers start: 52
  outliers final: 35
  residues processed: 171
  average time/residue: 0.0781
  time to fit residues: 20.0407
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  : 0.334 
-------------------------------------------------------------------------------
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  180 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  224 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  403 GLU
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  540 VAL
Chi-restraints excluded: chain A residue  561 HIS
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   38 VAL
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  149 ILE
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  224 VAL
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  257 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  448 ILE
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 88 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 95 optimal weight:   10.0000
   chunk 61 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0980
   chunk 93 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.4642 r_free = 0.4642 target = 0.207294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.145338 restraints weight = 12818.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.144435 restraints weight = 7033.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.145289 restraints weight = 4616.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.146061 restraints weight = 4154.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.146361 restraints weight = 3652.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2667

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= 0.155
  Angle     :  0.746  14.350  12094  Z= 0.365
  Chirality :  0.044   0.305   1464
  Planarity :  0.005   0.084   1518
  Dihedral  :  5.422  46.305   1227
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  6.23 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 27.59 %
    Favored  : 66.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.26), residues: 1140
  helix:  2.12 (0.19), residues: 758
  sheet:  1.30 (0.65), residues: 70
  loop : -3.59 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 486 
 TYR   0.022   0.001   TYR B 114 
 PHE   0.019   0.001   PHE B 390 
 TRP   0.008   0.001   TRP B 164 
 HIS   0.003   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8936)
  covalent geometry    : angle       0.74601 (12094)
  hydrogen bonds       : bond        0.04360 (  592)
  hydrogen bonds       : angle       4.18402 ( 1752)

*********************** 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
  190 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 133
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7747 (tptt)
REVERT: A  122 GLU cc_start: 0.7835 (tp30) cc_final: 0.7532 (tm-30)
REVERT: A  169 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8751 (mm)
REVERT: A  271 MET cc_start: 0.8371 (mmt) cc_final: 0.8143 (mmm)
REVERT: A  317 MET cc_start: 0.8674 (tpp) cc_final: 0.8294 (mmt)
REVERT: A  428 SER cc_start: 0.8569 (t) cc_final: 0.7943 (p)
REVERT: A  454 MET cc_start: 0.8007 (mmm) cc_final: 0.7800 (mmp)
REVERT: B   29 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7730 (mp)
REVERT: B   61 ASN cc_start: 0.4469 (OUTLIER) cc_final: 0.3937 (t0)
REVERT: B  126 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6652 (mtm110)
REVERT: B  160 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7969 (m-80)
REVERT: B  169 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8717 (mm)
REVERT: B  249 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7205 (mp)
REVERT: B  259 MET cc_start: 0.8672 (tpp) cc_final: 0.8302 (tpp)
REVERT: B  290 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6699 (mp)
REVERT: B  436 CYS cc_start: 0.7757 (t) cc_final: 0.6552 (p)
REVERT: B  494 LEU cc_start: 0.7875 (mt) cc_final: 0.7634 (tt)
REVERT: B  501 MET cc_start: 0.8334 (tmm) cc_final: 0.7792 (tmm)
  outliers start: 57
  outliers final: 40
  residues processed: 176
  average time/residue: 0.0735
  time to fit residues: 19.6078
Evaluate side-chains
  181 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 132
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
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  180 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  224 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  403 GLU
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  448 ILE
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  561 HIS
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   38 VAL
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   67 ILE
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  149 ILE
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  169 LEU
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  224 VAL
Chi-restraints excluded: chain B residue  249 LEU
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  304 PHE
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  387 LEU
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 3 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 54 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 94 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4661 r_free = 0.4661 target = 0.209318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.148044 restraints weight = 12720.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.148147 restraints weight = 6011.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.148045 restraints weight = 4068.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.149088 restraints weight = 3898.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.149485 restraints weight = 3313.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8936  Z= 0.149
  Angle     :  0.761  14.401  12094  Z= 0.372
  Chirality :  0.044   0.311   1464
  Planarity :  0.005   0.083   1518
  Dihedral  :  5.412  46.419   1227
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  5.96 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 28.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.26), residues: 1140
  helix:  2.12 (0.19), residues: 756
  sheet:  1.40 (0.65), residues: 70
  loop : -3.53 (0.30), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 389 
 TYR   0.022   0.001   TYR B 114 
 PHE   0.019   0.001   PHE A 348 
 TRP   0.011   0.001   TRP B 164 
 HIS   0.003   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8936)
  covalent geometry    : angle       0.76108 (12094)
  hydrogen bonds       : bond        0.04268 (  592)
  hydrogen bonds       : angle       4.14453 ( 1752)

********************** 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
  180 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 131
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7692 (tptt)
REVERT: A  122 GLU cc_start: 0.7790 (tp30) cc_final: 0.7501 (tm-30)
REVERT: A  169 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8711 (mm)
REVERT: A  271 MET cc_start: 0.8355 (mmt) cc_final: 0.7957 (mmm)
REVERT: A  317 MET cc_start: 0.8615 (tpp) cc_final: 0.8227 (mmt)
REVERT: A  411 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8978 (tm-30)
REVERT: A  428 SER cc_start: 0.8507 (t) cc_final: 0.7960 (p)
REVERT: A  501 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8120 (tmm)
REVERT: B   29 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7634 (mp)
REVERT: B   61 ASN cc_start: 0.4558 (OUTLIER) cc_final: 0.4046 (t0)
REVERT: B  126 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6446 (mtm110)
REVERT: B  130 ASP cc_start: 0.7388 (m-30) cc_final: 0.6984 (m-30)
REVERT: B  160 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7972 (m-80)
REVERT: B  169 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8606 (mm)
REVERT: B  249 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7203 (mp)
REVERT: B  290 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6605 (mp)
REVERT: B  436 CYS cc_start: 0.7778 (t) cc_final: 0.6621 (p)
REVERT: B  494 LEU cc_start: 0.7939 (mt) cc_final: 0.7733 (tt)
REVERT: B  501 MET cc_start: 0.8329 (tmm) cc_final: 0.7778 (tmm)
  outliers start: 49
  outliers final: 35
  residues processed: 168
  average time/residue: 0.0750
  time to fit residues: 18.9734
Evaluate side-chains
  173 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 128
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  180 ILE
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  224 VAL
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  403 GLU
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  501 MET
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   29 LEU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   46 ILE
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  149 ILE
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  169 LEU
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  257 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  290 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:   30.0000
   chunk 62 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 84 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 94 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   chunk 108 optimal weight:   40.0000
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.4650 r_free = 0.4650 target = 0.208283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.147273 restraints weight = 12594.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.146526 restraints weight = 6735.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.147165 restraints weight = 4341.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.147923 restraints weight = 4003.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.148138 restraints weight = 3590.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8936  Z= 0.150
  Angle     :  0.763  13.125  12094  Z= 0.372
  Chirality :  0.044   0.326   1464
  Planarity :  0.005   0.082   1518
  Dihedral  :  5.370  46.912   1227
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  5.96 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 27.70 %
    Favored  : 66.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.26), residues: 1140
  helix:  2.22 (0.19), residues: 744
  sheet:  1.43 (0.65), residues: 70
  loop : -3.42 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 389 
 TYR   0.021   0.001   TYR B 114 
 PHE   0.019   0.001   PHE A 348 
 TRP   0.010   0.001   TRP B 164 
 HIS   0.003   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8936)
  covalent geometry    : angle       0.76298 (12094)
  hydrogen bonds       : bond        0.04217 (  592)
  hydrogen bonds       : angle       4.13467 ( 1752)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1651.13 seconds
wall clock time: 29 minutes 18.76 seconds (1758.76 seconds total)