Starting phenix.real_space_refine
on Tue May 13 15:49:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ymm_39399/05_2025/8ymm_39399_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ymm_39399/05_2025/8ymm_39399.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ymm_39399/05_2025/8ymm_39399.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ymm_39399/05_2025/8ymm_39399.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ymm_39399/05_2025/8ymm_39399_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ymm_39399/05_2025/8ymm_39399_neut.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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      52      5.16       5
     C    7070      2.51       5
     N    1758      2.21       5
     O    1830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10710
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 664, 5346
          Classifications: {'peptide': 664}
          Link IDs: {'PTRANS': 35, 'TRANS': 628}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 664, 5346
          Classifications: {'peptide': 664}
          Link IDs: {'PTRANS': 35, 'TRANS': 628}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'PEE': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'PEE': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 12.89, per 1000 atoms: 1.20
  Number of scatterers: 10710
  At special positions: 0
  Unit cell: (148.75, 81.55, 85.05, 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      52     16.00
     O    1830      8.00
     N    1758      7.00
     C    7070      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: 3.03
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2524

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 2 sheets defined
      73.8% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 31
      removed outlier: 3.649A  pdb=" N   GLN A  31 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 36
      removed outlier: 4.007A  pdb=" N   ARG A  36 " --> pdb=" O   PRO A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 45
      removed outlier: 3.660A  pdb=" N   TYR A  43 " --> pdb=" O   PHE A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.516A  pdb=" N   PHE A  72 " --> pdb=" O   TYR A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 80
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 92 through 117
      removed outlier: 3.966A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 160 through 194
    Processing helix  chain 'A' and resid 198 through 202
      removed outlier: 4.115A  pdb=" N   PHE A 202 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 198 through 202'
    Processing helix  chain 'A' and resid 216 through 228
    Processing helix  chain 'A' and resid 242 through 259
      removed outlier: 3.863A  pdb=" N   LEU A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 267
      removed outlier: 4.535A  pdb=" N   TYR A 266 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 296
    Processing helix  chain 'A' and resid 296 through 315
    Processing helix  chain 'A' and resid 330 through 339
    Processing helix  chain 'A' and resid 361 through 366
      removed outlier: 3.752A  pdb=" N   ALA A 366 " --> pdb=" O   PRO A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 389
    Processing helix  chain 'A' and resid 390 through 407
    Processing helix  chain 'A' and resid 433 through 441
      removed outlier: 3.627A  pdb=" N   PHE A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 454
    Processing helix  chain 'A' and resid 457 through 477
    Processing helix  chain 'A' and resid 477 through 483
    Processing helix  chain 'A' and resid 487 through 496
    Processing helix  chain 'A' and resid 500 through 510
      removed outlier: 3.582A  pdb=" N   LYS A 504 " --> pdb=" O   ASN A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 525
    Processing helix  chain 'A' and resid 526 through 535
    Processing helix  chain 'A' and resid 535 through 547
    Processing helix  chain 'A' and resid 566 through 588
      Proline residue:  A 572  - end of helix
      Proline residue:  A 586  - end of helix
    Processing helix  chain 'A' and resid 590 through 613
      removed outlier: 4.316A  pdb=" N   PHE A 594 " --> pdb=" O   MET A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 650
    Processing helix  chain 'A' and resid 655 through 660
    Processing helix  chain 'A' and resid 660 through 677
      removed outlier: 4.196A  pdb=" N   VAL A 664 " --> pdb=" O   ILE A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 683
      removed outlier: 3.696A  pdb=" N   VAL A 682 " --> pdb=" O   GLU A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 700
    Processing helix  chain 'A' and resid 704 through 711
      removed outlier: 3.873A  pdb=" N   TYR A 708 " --> pdb=" O   ASN A 704 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASP A 711 " --> pdb=" O   GLY A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 714
      No H-bonds generated for 'chain 'A' and resid 712 through 714'
    Processing helix  chain 'B' and resid 3 through 31
      removed outlier: 3.649A  pdb=" N   GLN B  31 " --> pdb=" O   PHE B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 36
      removed outlier: 4.007A  pdb=" N   ARG B  36 " --> pdb=" O   PRO B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 45
      removed outlier: 3.660A  pdb=" N   TYR B  43 " --> pdb=" O   PHE B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 73
      removed outlier: 3.516A  pdb=" N   PHE B  72 " --> pdb=" O   TYR B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 80
    Processing helix  chain 'B' and resid 83 through 91
    Processing helix  chain 'B' and resid 92 through 117
      removed outlier: 3.966A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 160 through 194
    Processing helix  chain 'B' and resid 198 through 202
      removed outlier: 4.115A  pdb=" N   PHE B 202 " --> pdb=" O   ARG B 198 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 198 through 202'
    Processing helix  chain 'B' and resid 216 through 228
    Processing helix  chain 'B' and resid 242 through 259
      removed outlier: 3.863A  pdb=" N   LEU B 259 " --> pdb=" O   LEU B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 267
      removed outlier: 4.535A  pdb=" N   TYR B 266 " --> pdb=" O   TYR B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 296
    Processing helix  chain 'B' and resid 296 through 315
    Processing helix  chain 'B' and resid 330 through 339
    Processing helix  chain 'B' and resid 361 through 366
      removed outlier: 3.752A  pdb=" N   ALA B 366 " --> pdb=" O   PRO B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 389
    Processing helix  chain 'B' and resid 390 through 407
    Processing helix  chain 'B' and resid 433 through 441
      removed outlier: 3.627A  pdb=" N   PHE B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 454
    Processing helix  chain 'B' and resid 457 through 477
    Processing helix  chain 'B' and resid 477 through 483
    Processing helix  chain 'B' and resid 487 through 496
    Processing helix  chain 'B' and resid 500 through 510
      removed outlier: 3.584A  pdb=" N   LYS B 504 " --> pdb=" O   ASN B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 525
    Processing helix  chain 'B' and resid 526 through 535
    Processing helix  chain 'B' and resid 535 through 547
    Processing helix  chain 'B' and resid 566 through 588
      Proline residue:  B 572  - end of helix
      Proline residue:  B 586  - end of helix
    Processing helix  chain 'B' and resid 590 through 613
      removed outlier: 4.316A  pdb=" N   PHE B 594 " --> pdb=" O   MET B 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 650
    Processing helix  chain 'B' and resid 655 through 660
    Processing helix  chain 'B' and resid 660 through 677
      removed outlier: 4.196A  pdb=" N   VAL B 664 " --> pdb=" O   ILE B 660 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 678 through 683
      removed outlier: 3.696A  pdb=" N   VAL B 682 " --> pdb=" O   GLU B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 685 through 700
    Processing helix  chain 'B' and resid 704 through 711
      removed outlier: 3.873A  pdb=" N   TYR B 708 " --> pdb=" O   ASN B 704 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASP B 711 " --> pdb=" O   GLY B 707 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 714
      No H-bonds generated for 'chain 'B' and resid 712 through 714'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 238 through 240
      removed outlier: 4.796A  pdb=" N   VAL A 239 " --> pdb=" O   MET A 321 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 238 through 240
      removed outlier: 4.796A  pdb=" N   VAL B 239 " --> pdb=" O   MET B 321 " (cutoff:3.500A)

    662 hydrogen bonds defined for protein.
    1962 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: 3.39

  Time building geometry restraints manager: 3.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2469
        1.33 -     1.45: 2331
        1.45 -     1.57: 6110
        1.57 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 11002
  Sorted by residual:
  bond pdb=" CA  ILE B 392 "
       pdb=" CB  ILE B 392 "
    ideal  model  delta    sigma   weight residual
    1.539  1.563 -0.024 5.40e-03 3.43e+04 2.04e+01
  bond pdb=" CA  ILE A 392 "
       pdb=" CB  ILE A 392 "
    ideal  model  delta    sigma   weight residual
    1.539  1.563 -0.024 5.40e-03 3.43e+04 2.04e+01
  bond pdb=" C   TYR A 684 "
       pdb=" N   PRO A 685 "
    ideal  model  delta    sigma   weight residual
    1.331  1.378 -0.047 1.20e-02 6.94e+03 1.53e+01
  bond pdb=" C   TYR B 684 "
       pdb=" N   PRO B 685 "
    ideal  model  delta    sigma   weight residual
    1.331  1.378 -0.047 1.20e-02 6.94e+03 1.53e+01
  bond pdb=" CA  ILE B 510 "
       pdb=" CB  ILE B 510 "
    ideal  model  delta    sigma   weight residual
    1.537  1.555 -0.018 5.00e-03 4.00e+04 1.33e+01
  ... (remaining 10997 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.77: 14251
        2.77 -     5.53: 547
        5.53 -     8.30: 126
        8.30 -    11.07: 22
       11.07 -    13.84: 6
  Bond angle restraints: 14952
  Sorted by residual:
  angle pdb=" N   TYR A  69 "
        pdb=" CA  TYR A  69 "
        pdb=" C   TYR A  69 "
      ideal   model   delta    sigma   weight residual
     113.88  105.92    7.96 1.23e+00 6.61e-01 4.18e+01
  angle pdb=" N   TYR B  69 "
        pdb=" CA  TYR B  69 "
        pdb=" C   TYR B  69 "
      ideal   model   delta    sigma   weight residual
     113.88  105.92    7.96 1.23e+00 6.61e-01 4.18e+01
  angle pdb=" N   LYS B 318 "
        pdb=" CA  LYS B 318 "
        pdb=" C   LYS B 318 "
      ideal   model   delta    sigma   weight residual
     114.12  105.61    8.51 1.39e+00 5.18e-01 3.75e+01
  angle pdb=" N   LYS A 318 "
        pdb=" CA  LYS A 318 "
        pdb=" C   LYS A 318 "
      ideal   model   delta    sigma   weight residual
     114.12  105.61    8.51 1.39e+00 5.18e-01 3.75e+01
  angle pdb=" N   ILE B 296 "
        pdb=" CA  ILE B 296 "
        pdb=" C   ILE B 296 "
      ideal   model   delta    sigma   weight residual
     109.34  121.57  -12.23 2.08e+00 2.31e-01 3.46e+01
  ... (remaining 14947 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.20: 5303
       22.20 -    44.40: 729
       44.40 -    66.60: 426
       66.60 -    88.80: 26
       88.80 -   111.00: 2
  Dihedral angle restraints: 6486
    sinusoidal: 2584
      harmonic: 3902
  Sorted by residual:
  dihedral pdb=" C   HIS B 715 "
           pdb=" N   HIS B 715 "
           pdb=" CA  HIS B 715 "
           pdb=" CB  HIS B 715 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.15   15.55     0      2.50e+00 1.60e-01 3.87e+01
  dihedral pdb=" C   HIS A 715 "
           pdb=" N   HIS A 715 "
           pdb=" CA  HIS A 715 "
           pdb=" CB  HIS A 715 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.15   15.55     0      2.50e+00 1.60e-01 3.87e+01
  dihedral pdb=" C   ILE B 510 "
           pdb=" N   ILE B 510 "
           pdb=" CA  ILE B 510 "
           pdb=" CB  ILE B 510 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.25   15.25     0      2.50e+00 1.60e-01 3.72e+01
  ... (remaining 6483 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1347
       0.106 -    0.213: 229
       0.213 -    0.319: 72
       0.319 -    0.426: 20
       0.426 -    0.532: 10
  Chirality restraints: 1678
  Sorted by residual:
  chirality pdb=" CA  TRP B 625 "
            pdb=" N   TRP B 625 "
            pdb=" C   TRP B 625 "
            pdb=" CB  TRP B 625 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.07e+00
  chirality pdb=" CA  TRP A 625 "
            pdb=" N   TRP A 625 "
            pdb=" C   TRP A 625 "
            pdb=" CB  TRP A 625 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.07e+00
  chirality pdb=" CA  ILE A 510 "
            pdb=" N   ILE A 510 "
            pdb=" C   ILE A 510 "
            pdb=" CB  ILE A 510 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.91    0.53 2.00e-01 2.50e+01 6.94e+00
  ... (remaining 1675 not shown)

  Planarity restraints: 1872
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 625 "    0.044 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO B 626 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 626 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 626 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 625 "   -0.044 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO A 626 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 626 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 626 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 502 "   -0.038 5.00e-02 4.00e+02   5.82e-02 5.43e+00
        pdb=" N   PRO B 503 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 503 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 503 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1869 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.39: 9
        2.39 -     3.02: 6250
        3.02 -     3.65: 17385
        3.65 -     4.27: 29674
        4.27 -     4.90: 44709
  Nonbonded interactions: 98027
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 676 "
            pdb=" OD1 ASN B 345 "
     model   vdw
     1.766 3.120
  nonbonded pdb=" OD1 ASN A 345 "
            pdb=" NH1 ARG B 676 "
     model   vdw
     1.766 3.120
  nonbonded pdb=" OD1 ASN A 345 "
            pdb=" CZ  ARG B 676 "
     model   vdw
     2.066 3.270
  nonbonded pdb=" CZ  ARG A 676 "
            pdb=" OD1 ASN B 345 "
     model   vdw
     2.066 3.270
  nonbonded pdb=" O   GLN A 339 "
            pdb=" O   GLN B 339 "
     model   vdw
     2.182 3.040
  ... (remaining 98022 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: 0.05
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             32.000
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          2.590
  Check model and map are aligned:         0.080
  Set scattering table:                    0.150
  Process input model:                     33.430
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.050
  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:13.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   82.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6576
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      :  0.008   0.047  11002  Z= 0.592
  Angle     :  1.352  13.835  14952  Z= 0.864
  Chirality :  0.104   0.532   1678
  Planarity :  0.008   0.066   1872
  Dihedral  : 24.374 111.002   3962
  Min Nonbonded Distance : 1.766

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  1.67 %
    Allowed  :  9.73 %
    Favored  : 88.60 %
  Rotamer:
    Outliers : 34.68 %
    Allowed  : 15.14 %
    Favored  : 50.18 %
  Cbeta Deviations :  1.27 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.17 (0.20), residues: 1316
  helix: -1.33 (0.15), residues: 858
  sheet: -3.58 (0.77), residues: 36
  loop : -3.44 (0.27), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 625 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.021   0.003   PHE A  72 
 TYR   0.012   0.002   TYR A 295 
 ARG   0.004   0.001   ARG A  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17897 (  662)
  hydrogen bonds       : angle       7.69104 ( 1962)
  covalent geometry    : bond        0.00801 (11002)
  covalent geometry    : angle       1.35230 (14952)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  636 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 394
    poor density    : 242
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7585 (tttt)
REVERT: A   85 ARG cc_start: 0.5687 (OUTLIER) cc_final: 0.5293 (tmt170)
REVERT: A  159 PHE cc_start: 0.3749 (OUTLIER) cc_final: 0.3443 (t80)
REVERT: A  228 ASN cc_start: 0.7032 (m110) cc_final: 0.6617 (m-40)
REVERT: A  258 TRP cc_start: 0.3263 (OUTLIER) cc_final: 0.2051 (t60)
REVERT: A  294 HIS cc_start: 0.1831 (OUTLIER) cc_final: 0.1038 (t-90)
REVERT: B   41 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7574 (tttt)
REVERT: B   85 ARG cc_start: 0.5710 (OUTLIER) cc_final: 0.5268 (tmt170)
REVERT: B  228 ASN cc_start: 0.7012 (m110) cc_final: 0.6641 (m-40)
REVERT: B  258 TRP cc_start: 0.3261 (OUTLIER) cc_final: 0.2077 (t60)
REVERT: B  294 HIS cc_start: 0.1801 (OUTLIER) cc_final: 0.1024 (t-90)
  outliers start: 394
  outliers final: 38
  residues processed: 530
  average time/residue: 1.0502
  time to fit residues: 604.6330
Evaluate side-chains
  179 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 132
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   49 SER
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  265 LYS
Chi-restraints excluded: chain A residue  268 ARG
Chi-restraints excluded: chain A residue  274 ARG
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  555 ASP
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  265 LYS
Chi-restraints excluded: chain B residue  268 ARG
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  294 HIS
Chi-restraints excluded: chain B residue  298 GLU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  533 ILE
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  553 GLU
Chi-restraints excluded: chain B residue  555 ASP
Chi-restraints excluded: chain B residue  565 ILE
Chi-restraints excluded: chain B residue  582 LEU
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  705 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0980
   chunk 103 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9990
   chunk 119 optimal weight:    0.8980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A  90 HIS
A 124 ASN
A 208 ASN
A 228 ASN
A 339 GLN
A 501 GLN
** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 573 GLN
A 575 GLN
A 609 GLN
A 615 ASN
A 616 GLN
B  74 HIS
B  90 HIS
B 124 ASN
B 208 ASN
B 228 ASN
B 339 GLN
B 501 GLN
** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 573 GLN
B 575 GLN
B 609 GLN
B 615 ASN
B 616 GLN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.185024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.124953 restraints weight = 11446.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.05
r_work: 0.3209 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11002  Z= 0.168
  Angle     :  0.753  11.750  14952  Z= 0.383
  Chirality :  0.048   0.269   1678
  Planarity :  0.007   0.058   1872
  Dihedral  : 10.736  78.430   1568
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.21 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  9.07 %
    Allowed  : 25.62 %
    Favored  : 65.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.23), residues: 1316
  helix:  0.45 (0.18), residues: 844
  sheet: -2.97 (0.75), residues: 34
  loop : -2.89 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 625 
 HIS   0.005   0.001   HIS A 651 
 PHE   0.022   0.002   PHE B 390 
 TYR   0.020   0.002   TYR B 295 
 ARG   0.008   0.001   ARG A  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04825 (  662)
  hydrogen bonds       : angle       5.49444 ( 1962)
  covalent geometry    : bond        0.00375 (11002)
  covalent geometry    : angle       0.75335 (14952)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 103
    poor density    : 150
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8010 (mp)
REVERT: A   85 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6911 (tpt170)
REVERT: A  123 VAL cc_start: 0.5750 (OUTLIER) cc_final: 0.5395 (m)
REVERT: A  159 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.5948 (t80)
REVERT: A  222 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7688 (tp30)
REVERT: A  258 TRP cc_start: 0.3476 (OUTLIER) cc_final: 0.2907 (t60)
REVERT: A  288 LYS cc_start: 0.1216 (OUTLIER) cc_final: 0.0617 (pmtt)
REVERT: A  436 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6540 (tttp)
REVERT: A  501 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.6121 (mm-40)
REVERT: A  682 VAL cc_start: 0.9110 (m) cc_final: 0.8813 (p)
REVERT: B   47 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.8000 (mp)
REVERT: B   85 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6933 (tpt170)
REVERT: B  222 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7676 (tp30)
REVERT: B  258 TRP cc_start: 0.3482 (OUTLIER) cc_final: 0.2906 (t60)
REVERT: B  288 LYS cc_start: 0.1214 (OUTLIER) cc_final: 0.0611 (pmtt)
REVERT: B  501 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.6149 (mm-40)
REVERT: B  682 VAL cc_start: 0.9103 (m) cc_final: 0.8798 (p)
  outliers start: 103
  outliers final: 26
  residues processed: 234
  average time/residue: 1.0263
  time to fit residues: 261.6077
Evaluate side-chains
  161 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 120
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  436 LYS
Chi-restraints excluded: chain A residue  501 GLN
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  654 SER
Chi-restraints excluded: chain A residue  700 GLU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  501 GLN
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  553 GLU
Chi-restraints excluded: chain B residue  565 ILE
Chi-restraints excluded: chain B residue  582 LEU
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  654 SER
Chi-restraints excluded: chain B residue  700 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9980
   chunk 108 optimal weight:    0.4980
   chunk 40 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 117 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 208 ASN
A 476 ASN
A 616 GLN
A 710 GLN
B  74 HIS
B 208 ASN
B 476 ASN
B 616 GLN
B 710 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.183209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.123607 restraints weight = 11846.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.03
r_work: 0.3218 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11002  Z= 0.152
  Angle     :  0.686  10.382  14952  Z= 0.343
  Chirality :  0.045   0.185   1678
  Planarity :  0.006   0.054   1872
  Dihedral  :  8.277  59.152   1506
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.36 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 27.64 %
    Favored  : 65.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.24), residues: 1316
  helix:  0.81 (0.18), residues: 874
  sheet: -2.80 (0.76), residues: 36
  loop : -2.94 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 625 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.020   0.001   PHE A 390 
 TYR   0.018   0.001   TYR A  43 
 ARG   0.005   0.000   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04284 (  662)
  hydrogen bonds       : angle       5.07471 ( 1962)
  covalent geometry    : bond        0.00339 (11002)
  covalent geometry    : angle       0.68573 (14952)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 141
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6929 (tpt170)
REVERT: A  163 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7996 (pt)
REVERT: A  222 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7803 (tp30)
REVERT: A  240 CYS cc_start: 0.8708 (p) cc_final: 0.8492 (p)
REVERT: A  254 LYS cc_start: 0.5702 (ttpt) cc_final: 0.5093 (tptt)
REVERT: A  258 TRP cc_start: 0.3582 (OUTLIER) cc_final: 0.3005 (t60)
REVERT: A  288 LYS cc_start: 0.1140 (OUTLIER) cc_final: 0.0269 (pmtt)
REVERT: A  295 TYR cc_start: 0.6014 (OUTLIER) cc_final: 0.5694 (m-80)
REVERT: A  318 LYS cc_start: 0.7678 (ptpt) cc_final: 0.7384 (pmmt)
REVERT: A  385 PHE cc_start: 0.7941 (m-80) cc_final: 0.7527 (m-80)
REVERT: A  435 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6261 (mt)
REVERT: A  436 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6378 (tttp)
REVERT: A  682 VAL cc_start: 0.9099 (m) cc_final: 0.8801 (p)
REVERT: B   85 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6918 (tpt170)
REVERT: B  222 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7797 (tp30)
REVERT: B  240 CYS cc_start: 0.8727 (p) cc_final: 0.8512 (p)
REVERT: B  254 LYS cc_start: 0.5699 (ttpt) cc_final: 0.5096 (tptt)
REVERT: B  258 TRP cc_start: 0.3583 (OUTLIER) cc_final: 0.3006 (t60)
REVERT: B  288 LYS cc_start: 0.1149 (OUTLIER) cc_final: 0.0267 (pmtt)
REVERT: B  295 TYR cc_start: 0.6008 (OUTLIER) cc_final: 0.5693 (m-80)
REVERT: B  318 LYS cc_start: 0.7709 (ptpt) cc_final: 0.7416 (pmmt)
REVERT: B  385 PHE cc_start: 0.7941 (m-80) cc_final: 0.7526 (m-80)
REVERT: B  435 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6260 (mt)
REVERT: B  682 VAL cc_start: 0.9101 (m) cc_final: 0.8804 (p)
  outliers start: 78
  outliers final: 35
  residues processed: 203
  average time/residue: 1.0413
  time to fit residues: 230.3170
Evaluate side-chains
  174 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 125
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  436 LYS
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  654 SER
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  295 TYR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  435 LEU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  553 GLU
Chi-restraints excluded: chain B residue  565 ILE
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  613 VAL
Chi-restraints excluded: chain B residue  654 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 12 optimal weight:    0.0370
   chunk 89 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 115 optimal weight:    9.9990
   chunk 91 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    1.5862

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 342 GLN
A 500 ASN
A 616 GLN
B  74 HIS
B 342 GLN
B 500 ASN
B 616 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.176186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.116219 restraints weight = 11663.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 1.99
r_work: 0.3111 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.4686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  11002  Z= 0.215
  Angle     :  0.703   8.197  14952  Z= 0.351
  Chirality :  0.049   0.324   1678
  Planarity :  0.006   0.052   1872
  Dihedral  :  7.543  59.935   1500
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.60 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 28.26 %
    Favored  : 64.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.24), residues: 1316
  helix:  0.94 (0.17), residues: 862
  sheet: -2.32 (0.78), residues: 36
  loop : -2.82 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 625 
 HIS   0.005   0.001   HIS B 670 
 PHE   0.016   0.002   PHE B 517 
 TYR   0.017   0.002   TYR B 577 
 ARG   0.005   0.001   ARG B 207 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04590 (  662)
  hydrogen bonds       : angle       4.99788 ( 1962)
  covalent geometry    : bond        0.00520 (11002)
  covalent geometry    : angle       0.70300 (14952)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 129
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6992 (tpt170)
REVERT: A  222 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7807 (tp30)
REVERT: A  228 ASN cc_start: 0.8708 (m-40) cc_final: 0.8300 (m110)
REVERT: A  254 LYS cc_start: 0.5676 (ttpt) cc_final: 0.5100 (tttt)
REVERT: A  258 TRP cc_start: 0.3636 (OUTLIER) cc_final: 0.3099 (t60)
REVERT: A  288 LYS cc_start: 0.1222 (OUTLIER) cc_final: 0.0357 (pmtt)
REVERT: A  295 TYR cc_start: 0.5954 (OUTLIER) cc_final: 0.5649 (m-80)
REVERT: A  682 VAL cc_start: 0.9156 (m) cc_final: 0.8901 (p)
REVERT: B   85 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6989 (tpt170)
REVERT: B  222 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7799 (tp30)
REVERT: B  228 ASN cc_start: 0.8723 (m-40) cc_final: 0.8309 (m110)
REVERT: B  254 LYS cc_start: 0.5676 (ttpt) cc_final: 0.5104 (tttt)
REVERT: B  258 TRP cc_start: 0.3640 (OUTLIER) cc_final: 0.3104 (t60)
REVERT: B  288 LYS cc_start: 0.1225 (OUTLIER) cc_final: 0.0358 (pmtt)
REVERT: B  295 TYR cc_start: 0.5945 (OUTLIER) cc_final: 0.5639 (m-80)
REVERT: B  682 VAL cc_start: 0.9153 (m) cc_final: 0.8886 (p)
  outliers start: 77
  outliers final: 40
  residues processed: 187
  average time/residue: 1.0127
  time to fit residues: 206.8148
Evaluate side-chains
  162 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 112
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  639 SER
Chi-restraints excluded: chain A residue  654 SER
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  295 TYR
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  553 GLU
Chi-restraints excluded: chain B residue  565 ILE
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  613 VAL
Chi-restraints excluded: chain B residue  639 SER
Chi-restraints excluded: chain B residue  654 SER
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  717 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 73 optimal weight:    0.3980
   chunk 127 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 92 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 208 ASN
A 616 GLN
B  74 HIS
B 208 ASN
B 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.177892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.123576 restraints weight = 11637.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.98
r_work: 0.3122 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.4888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11002  Z= 0.162
  Angle     :  0.661   7.850  14952  Z= 0.328
  Chirality :  0.046   0.274   1678
  Planarity :  0.005   0.051   1872
  Dihedral  :  7.109  59.315   1498
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.60 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 28.87 %
    Favored  : 65.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.24), residues: 1316
  helix:  1.05 (0.18), residues: 874
  sheet: -2.23 (0.79), residues: 36
  loop : -2.74 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 625 
 HIS   0.003   0.001   HIS B 670 
 PHE   0.014   0.001   PHE A 390 
 TYR   0.012   0.001   TYR A 577 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 (  662)
  hydrogen bonds       : angle       4.82596 ( 1962)
  covalent geometry    : bond        0.00386 (11002)
  covalent geometry    : angle       0.66074 (14952)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 128
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.1722 (OUTLIER) cc_final: 0.1483 (mp)
REVERT: A   85 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7026 (tpt170)
REVERT: A  222 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7861 (tp30)
REVERT: A  228 ASN cc_start: 0.8664 (m-40) cc_final: 0.8197 (m110)
REVERT: A  254 LYS cc_start: 0.5649 (ttpt) cc_final: 0.5078 (tttt)
REVERT: A  258 TRP cc_start: 0.3604 (OUTLIER) cc_final: 0.3087 (t60)
REVERT: A  318 LYS cc_start: 0.7652 (ptpt) cc_final: 0.7381 (pmmt)
REVERT: A  440 ILE cc_start: 0.8841 (mt) cc_final: 0.8638 (mm)
REVERT: A  682 VAL cc_start: 0.9154 (m) cc_final: 0.8879 (p)
REVERT: B   64 LEU cc_start: 0.1731 (OUTLIER) cc_final: 0.1490 (mp)
REVERT: B   85 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7015 (tpt170)
REVERT: B  222 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7849 (tp30)
REVERT: B  228 ASN cc_start: 0.8681 (m-40) cc_final: 0.8209 (m110)
REVERT: B  254 LYS cc_start: 0.5655 (ttpt) cc_final: 0.5081 (tttt)
REVERT: B  258 TRP cc_start: 0.3611 (OUTLIER) cc_final: 0.3091 (t60)
REVERT: B  318 LYS cc_start: 0.7656 (ptpt) cc_final: 0.7386 (pmmt)
REVERT: B  440 ILE cc_start: 0.8840 (mt) cc_final: 0.8638 (mm)
REVERT: B  682 VAL cc_start: 0.9150 (m) cc_final: 0.8868 (p)
  outliers start: 67
  outliers final: 37
  residues processed: 181
  average time/residue: 1.0944
  time to fit residues: 217.6637
Evaluate side-chains
  166 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 121
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  654 SER
Chi-restraints excluded: chain A residue  700 GLU
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  553 GLU
Chi-restraints excluded: chain B residue  565 ILE
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  613 VAL
Chi-restraints excluded: chain B residue  654 SER
Chi-restraints excluded: chain B residue  700 GLU
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  717 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 107 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 89 optimal weight:   20.0000
   chunk 111 optimal weight:    0.0670
   chunk 41 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A  74 HIS
A 616 GLN
B  14 ASN
B  74 HIS
B 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.180369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.123370 restraints weight = 11712.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 2.30
r_work: 0.3153 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.5104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  11002  Z= 0.140
  Angle     :  0.638   7.604  14952  Z= 0.316
  Chirality :  0.044   0.283   1678
  Planarity :  0.005   0.049   1872
  Dihedral  :  6.736  58.485   1490
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.29 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 28.61 %
    Favored  : 65.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.24), residues: 1316
  helix:  1.18 (0.18), residues: 874
  sheet: -2.02 (0.83), residues: 36
  loop : -2.70 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 625 
 HIS   0.002   0.001   HIS A 294 
 PHE   0.013   0.001   PHE A 390 
 TYR   0.012   0.001   TYR A 295 
 ARG   0.005   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  662)
  hydrogen bonds       : angle       4.77850 ( 1962)
  covalent geometry    : bond        0.00327 (11002)
  covalent geometry    : angle       0.63764 (14952)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 132
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7156 (mmp-170)
REVERT: A  222 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7854 (tp30)
REVERT: A  228 ASN cc_start: 0.8603 (m-40) cc_final: 0.8161 (m110)
REVERT: A  240 CYS cc_start: 0.8558 (p) cc_final: 0.8334 (p)
REVERT: A  254 LYS cc_start: 0.5632 (ttpt) cc_final: 0.5068 (tttt)
REVERT: A  258 TRP cc_start: 0.3581 (OUTLIER) cc_final: 0.3038 (t60)
REVERT: A  318 LYS cc_start: 0.7497 (ptpt) cc_final: 0.7199 (pmmt)
REVERT: A  430 LEU cc_start: 0.2530 (OUTLIER) cc_final: 0.2161 (mp)
REVERT: A  508 MET cc_start: 0.6511 (mtp) cc_final: 0.6154 (mpp)
REVERT: A  560 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5465 (ttp)
REVERT: A  682 VAL cc_start: 0.9121 (m) cc_final: 0.8827 (p)
REVERT: B   85 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7149 (mmp-170)
REVERT: B  222 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7843 (tp30)
REVERT: B  228 ASN cc_start: 0.8616 (m-40) cc_final: 0.8173 (m110)
REVERT: B  240 CYS cc_start: 0.8561 (p) cc_final: 0.8335 (p)
REVERT: B  254 LYS cc_start: 0.5640 (ttpt) cc_final: 0.5077 (tttt)
REVERT: B  258 TRP cc_start: 0.3582 (OUTLIER) cc_final: 0.3038 (t60)
REVERT: B  318 LYS cc_start: 0.7496 (ptpt) cc_final: 0.7200 (pmmt)
REVERT: B  430 LEU cc_start: 0.2476 (OUTLIER) cc_final: 0.2127 (mp)
REVERT: B  508 MET cc_start: 0.6501 (mtp) cc_final: 0.6142 (mpp)
REVERT: B  560 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5471 (ttp)
REVERT: B  682 VAL cc_start: 0.9125 (m) cc_final: 0.8825 (p)
  outliers start: 66
  outliers final: 30
  residues processed: 184
  average time/residue: 1.1253
  time to fit residues: 224.5784
Evaluate side-chains
  163 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 123
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  560 MET
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  700 GLU
Chi-restraints excluded: chain A residue  714 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  553 GLU
Chi-restraints excluded: chain B residue  560 MET
Chi-restraints excluded: chain B residue  565 ILE
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  613 VAL
Chi-restraints excluded: chain B residue  700 GLU
Chi-restraints excluded: chain B residue  714 ILE
Chi-restraints excluded: chain B residue  717 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 25 optimal weight:   20.0000
   chunk 82 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 115 optimal weight:    0.8980
   chunk 91 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 128 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 616 GLN
B  74 HIS
B 616 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.179858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.123235 restraints weight = 11933.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.17
r_work: 0.3114 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.5238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11002  Z= 0.151
  Angle     :  0.642   8.635  14952  Z= 0.317
  Chirality :  0.045   0.291   1678
  Planarity :  0.005   0.048   1872
  Dihedral  :  6.552  57.872   1488
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.14 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 28.79 %
    Favored  : 65.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.24), residues: 1316
  helix:  1.22 (0.17), residues: 874
  sheet: -2.04 (0.82), residues: 36
  loop : -2.69 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 625 
 HIS   0.003   0.001   HIS A 294 
 PHE   0.012   0.001   PHE A 390 
 TYR   0.010   0.001   TYR A 577 
 ARG   0.003   0.000   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03956 (  662)
  hydrogen bonds       : angle       4.73135 ( 1962)
  covalent geometry    : bond        0.00358 (11002)
  covalent geometry    : angle       0.64173 (14952)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 133
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.1791 (OUTLIER) cc_final: 0.1569 (mp)
REVERT: A   85 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7201 (mmp-170)
REVERT: A  222 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7831 (tp30)
REVERT: A  228 ASN cc_start: 0.8637 (m-40) cc_final: 0.8243 (m110)
REVERT: A  240 CYS cc_start: 0.8565 (p) cc_final: 0.8344 (p)
REVERT: A  254 LYS cc_start: 0.5644 (ttpt) cc_final: 0.5093 (tttt)
REVERT: A  258 TRP cc_start: 0.3647 (OUTLIER) cc_final: 0.3149 (t60)
REVERT: A  430 LEU cc_start: 0.2407 (OUTLIER) cc_final: 0.2130 (mp)
REVERT: A  560 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5575 (ttp)
REVERT: A  682 VAL cc_start: 0.9120 (m) cc_final: 0.8819 (p)
REVERT: B   64 LEU cc_start: 0.1806 (OUTLIER) cc_final: 0.1584 (mp)
REVERT: B   85 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7198 (mmp-170)
REVERT: B  222 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7826 (tp30)
REVERT: B  228 ASN cc_start: 0.8649 (m-40) cc_final: 0.8241 (m110)
REVERT: B  240 CYS cc_start: 0.8571 (p) cc_final: 0.8347 (p)
REVERT: B  254 LYS cc_start: 0.5645 (ttpt) cc_final: 0.5100 (tttt)
REVERT: B  258 TRP cc_start: 0.3649 (OUTLIER) cc_final: 0.3150 (t60)
REVERT: B  430 LEU cc_start: 0.2395 (OUTLIER) cc_final: 0.2120 (mp)
REVERT: B  560 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5581 (ttp)
REVERT: B  682 VAL cc_start: 0.9121 (m) cc_final: 0.8821 (p)
  outliers start: 64
  outliers final: 29
  residues processed: 181
  average time/residue: 1.1048
  time to fit residues: 217.3091
Evaluate side-chains
  160 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 119
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  560 MET
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  700 GLU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  553 GLU
Chi-restraints excluded: chain B residue  560 MET
Chi-restraints excluded: chain B residue  565 ILE
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  613 VAL
Chi-restraints excluded: chain B residue  700 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 86 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 208 ASN
A 616 GLN
B  74 HIS
B 208 ASN
B 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.177959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.120478 restraints weight = 11663.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.21
r_work: 0.3088 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.5330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11002  Z= 0.171
  Angle     :  0.664   8.983  14952  Z= 0.329
  Chirality :  0.046   0.311   1678
  Planarity :  0.005   0.048   1872
  Dihedral  :  6.543  57.154   1488
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.14 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 29.67 %
    Favored  : 65.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.24), residues: 1316
  helix:  1.25 (0.17), residues: 876
  sheet: -2.13 (0.81), residues: 36
  loop : -2.61 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 625 
 HIS   0.003   0.001   HIS B 294 
 PHE   0.012   0.001   PHE A 598 
 TYR   0.016   0.001   TYR B 542 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  662)
  hydrogen bonds       : angle       4.77825 ( 1962)
  covalent geometry    : bond        0.00411 (11002)
  covalent geometry    : angle       0.66377 (14952)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 130
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.1773 (OUTLIER) cc_final: 0.1495 (tp)
REVERT: A  182 GLU cc_start: 0.8742 (tt0) cc_final: 0.7984 (tt0)
REVERT: A  222 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7829 (tp30)
REVERT: A  228 ASN cc_start: 0.8683 (m-40) cc_final: 0.8308 (m110)
REVERT: A  254 LYS cc_start: 0.5630 (ttpt) cc_final: 0.5095 (tttt)
REVERT: A  258 TRP cc_start: 0.3657 (OUTLIER) cc_final: 0.3143 (t60)
REVERT: A  391 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6447 (mm)
REVERT: A  430 LEU cc_start: 0.2368 (OUTLIER) cc_final: 0.2137 (mp)
REVERT: A  508 MET cc_start: 0.6546 (mtp) cc_final: 0.6234 (mpp)
REVERT: A  560 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.5749 (ttp)
REVERT: A  682 VAL cc_start: 0.9146 (m) cc_final: 0.8856 (p)
REVERT: B   64 LEU cc_start: 0.1791 (OUTLIER) cc_final: 0.1509 (tp)
REVERT: B  182 GLU cc_start: 0.8734 (tt0) cc_final: 0.7973 (tt0)
REVERT: B  222 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7835 (tp30)
REVERT: B  228 ASN cc_start: 0.8698 (m-40) cc_final: 0.8303 (m110)
REVERT: B  254 LYS cc_start: 0.5641 (ttpt) cc_final: 0.5100 (tttt)
REVERT: B  258 TRP cc_start: 0.3664 (OUTLIER) cc_final: 0.3145 (t60)
REVERT: B  391 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6444 (mm)
REVERT: B  430 LEU cc_start: 0.2320 (OUTLIER) cc_final: 0.2116 (mp)
REVERT: B  508 MET cc_start: 0.6519 (mtp) cc_final: 0.6209 (mpp)
REVERT: B  560 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5759 (ttp)
REVERT: B  682 VAL cc_start: 0.9140 (m) cc_final: 0.8845 (p)
  outliers start: 55
  outliers final: 19
  residues processed: 169
  average time/residue: 1.0543
  time to fit residues: 194.5660
Evaluate side-chains
  150 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  560 MET
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  560 MET
Chi-restraints excluded: chain B residue  565 ILE
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  613 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 123 optimal weight:    0.5980
   chunk 117 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 102 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 616 GLN
B  74 HIS
B 616 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.180050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.122862 restraints weight = 11726.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.25
r_work: 0.3110 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.5520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11002  Z= 0.142
  Angle     :  0.641   9.232  14952  Z= 0.314
  Chirality :  0.045   0.336   1678
  Planarity :  0.005   0.048   1872
  Dihedral  :  5.695  56.382   1466
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.14 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 30.99 %
    Favored  : 65.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.24), residues: 1316
  helix:  1.33 (0.17), residues: 878
  sheet: -1.97 (0.83), residues: 36
  loop : -2.61 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 625 
 HIS   0.002   0.001   HIS A  90 
 PHE   0.012   0.001   PHE A 390 
 TYR   0.011   0.001   TYR A 295 
 ARG   0.008   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03813 (  662)
  hydrogen bonds       : angle       4.68208 ( 1962)
  covalent geometry    : bond        0.00337 (11002)
  covalent geometry    : angle       0.64100 (14952)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 125
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.1833 (OUTLIER) cc_final: 0.1571 (tp)
REVERT: A  222 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7869 (tp30)
REVERT: A  228 ASN cc_start: 0.8642 (m-40) cc_final: 0.8232 (m110)
REVERT: A  254 LYS cc_start: 0.5649 (ttpt) cc_final: 0.5127 (tttt)
REVERT: A  258 TRP cc_start: 0.3637 (OUTLIER) cc_final: 0.3138 (t60)
REVERT: A  508 MET cc_start: 0.6595 (mtp) cc_final: 0.6274 (mpp)
REVERT: A  682 VAL cc_start: 0.9126 (m) cc_final: 0.8815 (p)
REVERT: B   64 LEU cc_start: 0.1851 (OUTLIER) cc_final: 0.1587 (tp)
REVERT: B  222 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7873 (tp30)
REVERT: B  228 ASN cc_start: 0.8649 (m-40) cc_final: 0.8221 (m110)
REVERT: B  254 LYS cc_start: 0.5652 (ttpt) cc_final: 0.5125 (tttt)
REVERT: B  258 TRP cc_start: 0.3642 (OUTLIER) cc_final: 0.3142 (t60)
REVERT: B  508 MET cc_start: 0.6585 (mtp) cc_final: 0.6269 (mpp)
REVERT: B  588 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8219 (p)
REVERT: B  682 VAL cc_start: 0.9125 (m) cc_final: 0.8816 (p)
  outliers start: 38
  outliers final: 18
  residues processed: 155
  average time/residue: 1.0629
  time to fit residues: 180.0017
Evaluate side-chains
  148 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  565 ILE
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  613 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 123 optimal weight:    0.6980
   chunk 57 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 128 optimal weight:    0.0470
   chunk 87 optimal weight:    6.9990
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 616 GLN
B  74 HIS
B 616 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.180482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.122161 restraints weight = 11632.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.51
r_work: 0.3111 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.5602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11002  Z= 0.136
  Angle     :  0.632   9.380  14952  Z= 0.311
  Chirality :  0.045   0.335   1678
  Planarity :  0.005   0.048   1872
  Dihedral  :  5.565  53.819   1466
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.52 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 31.16 %
    Favored  : 65.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.24), residues: 1316
  helix:  1.40 (0.17), residues: 876
  sheet: -1.87 (0.83), residues: 36
  loop : -2.59 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 625 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.012   0.001   PHE A 390 
 TYR   0.010   0.001   TYR B 542 
 ARG   0.007   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03721 (  662)
  hydrogen bonds       : angle       4.65447 ( 1962)
  covalent geometry    : bond        0.00320 (11002)
  covalent geometry    : angle       0.63214 (14952)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 125
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.1829 (OUTLIER) cc_final: 0.1579 (tp)
REVERT: A  182 GLU cc_start: 0.8721 (tt0) cc_final: 0.7982 (tt0)
REVERT: A  222 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7849 (tp30)
REVERT: A  228 ASN cc_start: 0.8615 (m-40) cc_final: 0.8232 (m110)
REVERT: A  254 LYS cc_start: 0.5535 (ttpt) cc_final: 0.4786 (tttt)
REVERT: A  385 PHE cc_start: 0.7923 (m-80) cc_final: 0.7458 (m-80)
REVERT: A  508 MET cc_start: 0.6577 (mtp) cc_final: 0.6271 (mpp)
REVERT: A  560 MET cc_start: 0.6347 (OUTLIER) cc_final: 0.5747 (ttp)
REVERT: A  588 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8242 (p)
REVERT: A  682 VAL cc_start: 0.9112 (m) cc_final: 0.8802 (p)
REVERT: B   64 LEU cc_start: 0.1848 (OUTLIER) cc_final: 0.1593 (tp)
REVERT: B  182 GLU cc_start: 0.8723 (tt0) cc_final: 0.7983 (tt0)
REVERT: B  222 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7868 (tp30)
REVERT: B  228 ASN cc_start: 0.8627 (m-40) cc_final: 0.8218 (m110)
REVERT: B  254 LYS cc_start: 0.5545 (ttpt) cc_final: 0.4794 (tttt)
REVERT: B  385 PHE cc_start: 0.7935 (m-80) cc_final: 0.7464 (m-80)
REVERT: B  508 MET cc_start: 0.6596 (mtp) cc_final: 0.6290 (mpp)
REVERT: B  560 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.5753 (ttp)
REVERT: B  588 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8234 (p)
REVERT: B  682 VAL cc_start: 0.9114 (m) cc_final: 0.8800 (p)
  outliers start: 36
  outliers final: 19
  residues processed: 151
  average time/residue: 1.1451
  time to fit residues: 187.6761
Evaluate side-chains
  148 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  560 MET
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  181 TYR
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  560 MET
Chi-restraints excluded: chain B residue  565 ILE
Chi-restraints excluded: chain B residue  588 THR
Chi-restraints excluded: chain B residue  613 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 53 optimal weight:    0.0970
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0870
   chunk 35 optimal weight:    3.9990
   chunk 87 optimal weight:    7.9990
   chunk 60 optimal weight:    0.1980
   chunk 127 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.3756

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 616 GLN
B  74 HIS
B 342 GLN
B 616 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.182708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.123032 restraints weight = 11527.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.02
r_work: 0.3133 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.5753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11002  Z= 0.123
  Angle     :  0.617   9.268  14952  Z= 0.304
  Chirality :  0.044   0.333   1678
  Planarity :  0.005   0.048   1872
  Dihedral  :  5.389  52.557   1466
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.75 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 31.25 %
    Favored  : 65.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.24), residues: 1316
  helix:  1.46 (0.17), residues: 888
  sheet: -2.31 (0.86), residues: 30
  loop : -2.52 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 625 
 HIS   0.001   0.000   HIS B  90 
 PHE   0.012   0.001   PHE A 390 
 TYR   0.009   0.001   TYR B 577 
 ARG   0.010   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  662)
  hydrogen bonds       : angle       4.57980 ( 1962)
  covalent geometry    : bond        0.00286 (11002)
  covalent geometry    : angle       0.61709 (14952)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11672.78 seconds
wall clock time: 202 minutes 55.50 seconds (12175.50 seconds total)