Starting phenix.real_space_refine
on Mon Jul 28 21:46:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ymo_39401/07_2025/8ymo_39401_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ymo_39401/07_2025/8ymo_39401.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ymo_39401/07_2025/8ymo_39401.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ymo_39401/07_2025/8ymo_39401.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ymo_39401/07_2025/8ymo_39401_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ymo_39401/07_2025/8ymo_39401_neut.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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    7088      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 52 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10728
  Number of models: 1
  Model: ""
    Number of chains: 2
    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: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 18
          Unusual residues: {'PEE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2}
          Unresolved non-hydrogen planarities: 16
  Restraints were copied for chains:
    C
  Time building chain proxies: 16.37, per 1000 atoms: 1.53
  Number of scatterers: 10728
  At special positions: 0
  Unit cell: (150.15, 82.95, 89.6, 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    7088      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.71
  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:
      64 helices and 2 sheets defined
      71.1% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 31
    Processing helix  chain 'A' and resid 34 through 38
    Processing helix  chain 'A' and resid 39 through 45
      removed outlier: 3.672A  pdb=" N   TYR A  43 " --> pdb=" O   PHE A  39 " (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 120
      removed outlier: 3.929A  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 195
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 216 through 228
    Processing helix  chain 'A' and resid 242 through 259
      removed outlier: 4.525A  pdb=" N   LEU A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 267
      removed outlier: 4.328A  pdb=" N   TYR A 266 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 315
      removed outlier: 6.088A  pdb=" N   ALA A 297 " --> pdb=" O   GLU A 293 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   GLU A 298 " --> pdb=" O   HIS A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 339
    Processing helix  chain 'A' and resid 361 through 367
    Processing helix  chain 'A' and resid 368 through 408
      removed outlier: 3.701A  pdb=" N   THR A 373 " --> pdb=" O   TYR A 369 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   VAL A 374 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ILE A 392 " --> pdb=" O   PHE A 388 " (cutoff:3.500A)
      Proline residue:  A 393  - end of helix
    Processing helix  chain 'A' and resid 428 through 439
    Processing helix  chain 'A' and resid 441 through 454
    Processing helix  chain 'A' and resid 457 through 478
    Processing helix  chain 'A' and resid 489 through 496
    Processing helix  chain 'A' and resid 501 through 506
      removed outlier: 3.769A  pdb=" N   THR A 505 " --> pdb=" O   GLN A 501 " (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
      removed outlier: 3.602A  pdb=" N   ALA A 547 " --> pdb=" O   HIS A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 585
      Proline residue:  A 572  - end of helix
    Processing helix  chain 'A' and resid 590 through 613
      removed outlier: 4.377A  pdb=" N   PHE A 594 " --> pdb=" O   MET A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 647
    Processing helix  chain 'A' and resid 655 through 660
    Processing helix  chain 'A' and resid 660 through 677
      removed outlier: 3.989A  pdb=" N   VAL A 664 " --> pdb=" O   ILE A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 683
      removed outlier: 3.510A  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: 3.573A  pdb=" N   TYR A 708 " --> pdb=" O   ASN A 704 " (cutoff:3.500A)
      removed outlier: 4.318A  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 'C' and resid 3 through 31
    Processing helix  chain 'C' and resid 34 through 38
    Processing helix  chain 'C' and resid 39 through 45
      removed outlier: 3.672A  pdb=" N   TYR C  43 " --> pdb=" O   PHE C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 80
    Processing helix  chain 'C' and resid 83 through 91
    Processing helix  chain 'C' and resid 92 through 120
      removed outlier: 3.929A  pdb=" N   TYR C 102 " --> pdb=" O   TYR C  98 " (cutoff:3.500A)
      Proline residue:  C 111  - end of helix
    Processing helix  chain 'C' and resid 160 through 195
    Processing helix  chain 'C' and resid 198 through 201
    Processing helix  chain 'C' and resid 216 through 228
    Processing helix  chain 'C' and resid 242 through 259
      removed outlier: 4.525A  pdb=" N   LEU C 259 " --> pdb=" O   LEU C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 267
      removed outlier: 4.328A  pdb=" N   TYR C 266 " --> pdb=" O   TYR C 262 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 315
      removed outlier: 6.088A  pdb=" N   ALA C 297 " --> pdb=" O   GLU C 293 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   GLU C 298 " --> pdb=" O   HIS C 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 339
    Processing helix  chain 'C' and resid 361 through 367
    Processing helix  chain 'C' and resid 368 through 408
      removed outlier: 3.701A  pdb=" N   THR C 373 " --> pdb=" O   TYR C 369 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   VAL C 374 " --> pdb=" O   VAL C 370 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ILE C 392 " --> pdb=" O   PHE C 388 " (cutoff:3.500A)
      Proline residue:  C 393  - end of helix
    Processing helix  chain 'C' and resid 428 through 439
    Processing helix  chain 'C' and resid 441 through 454
    Processing helix  chain 'C' and resid 457 through 478
    Processing helix  chain 'C' and resid 489 through 496
    Processing helix  chain 'C' and resid 501 through 506
      removed outlier: 3.769A  pdb=" N   THR C 505 " --> pdb=" O   GLN C 501 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 513 through 525
    Processing helix  chain 'C' and resid 526 through 535
    Processing helix  chain 'C' and resid 535 through 547
      removed outlier: 3.602A  pdb=" N   ALA C 547 " --> pdb=" O   HIS C 543 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 566 through 585
      Proline residue:  C 572  - end of helix
    Processing helix  chain 'C' and resid 590 through 613
      removed outlier: 4.377A  pdb=" N   PHE C 594 " --> pdb=" O   MET C 590 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 624 through 647
    Processing helix  chain 'C' and resid 655 through 660
    Processing helix  chain 'C' and resid 660 through 677
      removed outlier: 3.989A  pdb=" N   VAL C 664 " --> pdb=" O   ILE C 660 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 678 through 683
      removed outlier: 3.510A  pdb=" N   VAL C 682 " --> pdb=" O   GLU C 678 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 685 through 700
    Processing helix  chain 'C' and resid 704 through 711
      removed outlier: 3.573A  pdb=" N   TYR C 708 " --> pdb=" O   ASN C 704 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ASP C 711 " --> pdb=" O   GLY C 707 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 712 through 714
      No H-bonds generated for 'chain 'C' and resid 712 through 714'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240
      removed outlier: 5.398A  pdb=" N   TYR A 233 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   SER A 327 " --> pdb=" O   TYR A 233 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   THR A 235 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   PHE A 325 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   GLN A 237 " --> pdb=" O   ALA A 323 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   ALA A 323 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   VAL A 239 " --> pdb=" O   MET A 321 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 233 through 240
      removed outlier: 5.398A  pdb=" N   TYR C 233 " --> pdb=" O   SER C 327 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   SER C 327 " --> pdb=" O   TYR C 233 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   THR C 235 " --> pdb=" O   PHE C 325 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   PHE C 325 " --> pdb=" O   THR C 235 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   GLN C 237 " --> pdb=" O   ALA C 323 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   ALA C 323 " --> pdb=" O   GLN C 237 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   VAL C 239 " --> pdb=" O   MET C 321 " (cutoff:3.500A)

    664 hydrogen bonds defined for protein.
    1944 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: 3.19

  Time building geometry restraints manager: 3.20 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1680
        1.32 -     1.44: 3066
        1.44 -     1.56: 6180
        1.56 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 11018
  Sorted by residual:
  bond pdb=" CA  ILE C 392 "
       pdb=" CB  ILE C 392 "
    ideal  model  delta    sigma   weight residual
    1.539  1.562 -0.023 5.40e-03 3.43e+04 1.81e+01
  bond pdb=" CA  ILE A 392 "
       pdb=" CB  ILE A 392 "
    ideal  model  delta    sigma   weight residual
    1.539  1.562 -0.023 5.40e-03 3.43e+04 1.81e+01
  bond pdb=" CA  VAL A 121 "
       pdb=" CB  VAL A 121 "
    ideal  model  delta    sigma   weight residual
    1.537  1.555 -0.019 5.00e-03 4.00e+04 1.38e+01
  bond pdb=" CA  VAL C 121 "
       pdb=" CB  VAL C 121 "
    ideal  model  delta    sigma   weight residual
    1.537  1.555 -0.019 5.00e-03 4.00e+04 1.38e+01
  bond pdb=" C   LYS A 537 "
       pdb=" N   PRO A 538 "
    ideal  model  delta    sigma   weight residual
    1.335  1.383 -0.048 1.36e-02 5.41e+03 1.24e+01
  ... (remaining 11013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.02: 14520
        3.02 -     6.04: 384
        6.04 -     9.06: 58
        9.06 -    12.09: 2
       12.09 -    15.11: 2
  Bond angle restraints: 14966
  Sorted by residual:
  angle pdb=" N   VAL C 482 "
        pdb=" CA  VAL C 482 "
        pdb=" C   VAL C 482 "
      ideal   model   delta    sigma   weight residual
     112.96  105.20    7.76 1.00e+00 1.00e+00 6.01e+01
  angle pdb=" N   VAL A 482 "
        pdb=" CA  VAL A 482 "
        pdb=" C   VAL A 482 "
      ideal   model   delta    sigma   weight residual
     112.96  105.20    7.76 1.00e+00 1.00e+00 6.01e+01
  angle pdb=" N   HIS C 651 "
        pdb=" CA  HIS C 651 "
        pdb=" C   HIS C 651 "
      ideal   model   delta    sigma   weight residual
     110.80  125.91  -15.11 2.13e+00 2.20e-01 5.03e+01
  angle pdb=" N   HIS A 651 "
        pdb=" CA  HIS A 651 "
        pdb=" C   HIS A 651 "
      ideal   model   delta    sigma   weight residual
     110.80  125.91  -15.11 2.13e+00 2.20e-01 5.03e+01
  angle pdb=" N   ILE A 440 "
        pdb=" CA  ILE A 440 "
        pdb=" C   ILE A 440 "
      ideal   model   delta    sigma   weight residual
     113.47  106.55    6.92 1.01e+00 9.80e-01 4.69e+01
  ... (remaining 14961 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 5088
       16.71 -    33.43: 618
       33.43 -    50.14: 500
       50.14 -    66.85: 258
       66.85 -    83.57: 34
  Dihedral angle restraints: 6498
    sinusoidal: 2596
      harmonic: 3902
  Sorted by residual:
  dihedral pdb=" C   PHE C 390 "
           pdb=" N   PHE C 390 "
           pdb=" CA  PHE C 390 "
           pdb=" CB  PHE C 390 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.33   18.73     0      2.50e+00 1.60e-01 5.61e+01
  dihedral pdb=" C   PHE A 390 "
           pdb=" N   PHE A 390 "
           pdb=" CA  PHE A 390 "
           pdb=" CB  PHE A 390 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.33   18.73     0      2.50e+00 1.60e-01 5.61e+01
  dihedral pdb=" N   PHE C 390 "
           pdb=" C   PHE C 390 "
           pdb=" CA  PHE C 390 "
           pdb=" CB  PHE C 390 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  141.46  -18.66     0      2.50e+00 1.60e-01 5.57e+01
  ... (remaining 6495 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.164: 1592
       0.164 -    0.327: 80
       0.327 -    0.491: 4
       0.491 -    0.654: 0
       0.654 -    0.818: 2
  Chirality restraints: 1678
  Sorted by residual:
  chirality pdb=" CA  PHE C 390 "
            pdb=" N   PHE C 390 "
            pdb=" C   PHE C 390 "
            pdb=" CB  PHE C 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.69    0.82 2.00e-01 2.50e+01 1.67e+01
  chirality pdb=" CA  PHE A 390 "
            pdb=" N   PHE A 390 "
            pdb=" C   PHE A 390 "
            pdb=" CB  PHE A 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.69    0.82 2.00e-01 2.50e+01 1.67e+01
  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    2.05    0.46 2.00e-01 2.50e+01 5.22e+00
  ... (remaining 1675 not shown)

  Planarity restraints: 1872
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 649 "    0.033 2.00e-02 2.50e+03   6.35e-02 4.04e+01
        pdb=" C   THR A 649 "   -0.110 2.00e-02 2.50e+03
        pdb=" O   THR A 649 "    0.040 2.00e-02 2.50e+03
        pdb=" N   LYS A 650 "    0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 649 "   -0.033 2.00e-02 2.50e+03   6.35e-02 4.04e+01
        pdb=" C   THR C 649 "    0.110 2.00e-02 2.50e+03
        pdb=" O   THR C 649 "   -0.040 2.00e-02 2.50e+03
        pdb=" N   LYS C 650 "   -0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 389 "    0.023 2.00e-02 2.50e+03   4.49e-02 2.02e+01
        pdb=" C   PHE C 389 "   -0.078 2.00e-02 2.50e+03
        pdb=" O   PHE C 389 "    0.028 2.00e-02 2.50e+03
        pdb=" N   PHE C 390 "    0.026 2.00e-02 2.50e+03
  ... (remaining 1869 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 143
        2.63 -     3.20: 9659
        3.20 -     3.76: 19153
        3.76 -     4.33: 27150
        4.33 -     4.90: 41068
  Nonbonded interactions: 97173
  Sorted by model distance:
  nonbonded pdb=" O   GLY C 648 "
            pdb=" NE2 HIS C 651 "
     model   vdw
     2.060 3.120
  nonbonded pdb=" O   GLY A 648 "
            pdb=" NE2 HIS A 651 "
     model   vdw
     2.060 3.120
  nonbonded pdb=" CG2 ILE C 483 "
            pdb=" CD1 PHE C 494 "
     model   vdw
     2.070 3.760
  nonbonded pdb=" CG2 ILE A 483 "
            pdb=" CD1 PHE A 494 "
     model   vdw
     2.070 3.760
  nonbonded pdb=" OD1 ASN A 241 "
            pdb=" CB  ALA A 366 "
     model   vdw
     2.119 3.460
  ... (remaining 97168 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 'C'
}

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:             278.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.840
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     36.620
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  329.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6435
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      :  0.007   0.048  11018  Z= 0.502
  Angle     :  1.186  15.107  14966  Z= 0.796
  Chirality :  0.081   0.818   1678
  Planarity :  0.006   0.064   1872
  Dihedral  : 24.230  83.566   3974
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  1.22 %
    Allowed  :  9.73 %
    Favored  : 89.06 %
  Rotamer:
    Outliers : 33.45 %
    Allowed  : 13.91 %
    Favored  : 52.64 %
  Cbeta Deviations :  0.32 %
  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: -2.93 (0.20), residues: 1316
  helix: -1.03 (0.15), residues: 860
  sheet: -3.43 (0.58), residues: 50
  loop : -3.61 (0.26), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 625 
 HIS   0.004   0.001   HIS C 651 
 PHE   0.011   0.002   PHE C 383 
 TYR   0.010   0.001   TYR C 618 
 ARG   0.002   0.000   ARG C 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18123 (  664)
  hydrogen bonds       : angle       7.48021 ( 1944)
  covalent geometry    : bond        0.00665 (11018)
  covalent geometry    : angle       1.18612 (14966)

*********************** 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
  596 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 380
    poor density    : 216
  time to evaluate  : 1.275 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7647 (tptt)
REVERT: A   61 PHE cc_start: 0.2961 (OUTLIER) cc_final: 0.1594 (t80)
REVERT: A  159 PHE cc_start: 0.3455 (OUTLIER) cc_final: 0.3231 (t80)
REVERT: A  278 LYS cc_start: 0.2467 (OUTLIER) cc_final: 0.0449 (ttmt)
REVERT: A  353 TRP cc_start: 0.6656 (m100) cc_final: 0.6257 (t60)
REVERT: A  555 ASP cc_start: 0.0128 (OUTLIER) cc_final: -0.0221 (t0)
REVERT: A  639 SER cc_start: 0.6352 (OUTLIER) cc_final: 0.6012 (p)
REVERT: A  654 SER cc_start: 0.4772 (OUTLIER) cc_final: 0.4185 (t)
REVERT: A  676 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7670 (tpt90)
REVERT: A  692 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.6855 (tttt)
REVERT: C   41 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7635 (tptt)
REVERT: C   61 PHE cc_start: 0.2929 (OUTLIER) cc_final: 0.1578 (t80)
REVERT: C  159 PHE cc_start: 0.3486 (OUTLIER) cc_final: 0.3225 (t80)
REVERT: C  278 LYS cc_start: 0.2460 (OUTLIER) cc_final: 0.0456 (ttmt)
REVERT: C  353 TRP cc_start: 0.6650 (m100) cc_final: 0.6258 (t60)
REVERT: C  555 ASP cc_start: 0.0134 (OUTLIER) cc_final: -0.0210 (t0)
REVERT: C  639 SER cc_start: 0.6373 (OUTLIER) cc_final: 0.6031 (p)
REVERT: C  654 SER cc_start: 0.4786 (OUTLIER) cc_final: 0.4181 (t)
REVERT: C  676 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7667 (tpt90)
REVERT: C  692 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.6865 (tttt)
  outliers start: 380
  outliers final: 18
  residues processed: 500
  average time/residue: 1.1559
  time to fit residues: 625.5517
Evaluate side-chains
  158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   49 SER
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  159 PHE
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  555 ASP
Chi-restraints excluded: chain A residue  639 SER
Chi-restraints excluded: chain A residue  654 SER
Chi-restraints excluded: chain A residue  676 ARG
Chi-restraints excluded: chain A residue  692 LYS
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue   49 SER
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  159 PHE
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  278 LYS
Chi-restraints excluded: chain C residue  295 TYR
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  439 LEU
Chi-restraints excluded: chain C residue  510 ILE
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  555 ASP
Chi-restraints excluded: chain C residue  639 SER
Chi-restraints excluded: chain C residue  654 SER
Chi-restraints excluded: chain C residue  676 ARG
Chi-restraints excluded: chain C residue  692 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0870
   chunk 103 optimal weight:   20.0000
   chunk 40 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 119 optimal weight:    0.9980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A  31 GLN
A  63 ASN
A  90 HIS
A 190 GLN
A 228 ASN
A 339 GLN
A 501 GLN
A 543 HIS
A 573 GLN
A 609 GLN
A 615 ASN
A 616 GLN
A 640 GLN
A 687 GLN
A 704 ASN
A 715 HIS
C  14 ASN
C  31 GLN
C  63 ASN
C  90 HIS
C 190 GLN
C 228 ASN
C 339 GLN
C 501 GLN
C 543 HIS
C 573 GLN
C 609 GLN
C 615 ASN
C 616 GLN
C 640 GLN
C 687 GLN
C 704 ASN
C 715 HIS

Total number of N/Q/H flips: 34

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.192436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.121953 restraints weight = 11002.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.09
r_work: 0.3203 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.4044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11018  Z= 0.185
  Angle     :  0.777  16.559  14966  Z= 0.387
  Chirality :  0.046   0.217   1678
  Planarity :  0.006   0.043   1872
  Dihedral  :  9.079  59.264   1542
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.21 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  8.63 %
    Allowed  : 24.65 %
    Favored  : 66.73 %
  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: -1.00 (0.23), residues: 1316
  helix:  0.79 (0.18), residues: 862
  sheet: -3.86 (0.49), residues: 46
  loop : -3.55 (0.26), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 625 
 HIS   0.004   0.001   HIS C 651 
 PHE   0.018   0.002   PHE A 494 
 TYR   0.027   0.002   TYR C  43 
 ARG   0.007   0.001   ARG A  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05231 (  664)
  hydrogen bonds       : angle       5.33515 ( 1944)
  covalent geometry    : bond        0.00401 (11018)
  covalent geometry    : angle       0.77652 (14966)

*********************** 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
  224 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 126
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 LYS cc_start: 0.5984 (OUTLIER) cc_final: 0.5655 (mttp)
REVERT: A  278 LYS cc_start: 0.0632 (OUTLIER) cc_final: 0.0086 (ttmt)
REVERT: A  318 LYS cc_start: 0.7984 (pttp) cc_final: 0.7771 (pmtt)
REVERT: A  353 TRP cc_start: 0.8237 (m100) cc_final: 0.7173 (t60)
REVERT: A  508 MET cc_start: 0.2926 (OUTLIER) cc_final: 0.1736 (mmp)
REVERT: A  555 ASP cc_start: 0.3690 (OUTLIER) cc_final: 0.2786 (t0)
REVERT: A  671 ARG cc_start: 0.7215 (mtp-110) cc_final: 0.6787 (mmm160)
REVERT: A  676 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8043 (tpt90)
REVERT: C  254 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5667 (mttp)
REVERT: C  278 LYS cc_start: 0.0632 (OUTLIER) cc_final: 0.0086 (ttmt)
REVERT: C  318 LYS cc_start: 0.7979 (pttp) cc_final: 0.7768 (pmtt)
REVERT: C  353 TRP cc_start: 0.8233 (m100) cc_final: 0.7177 (t60)
REVERT: C  508 MET cc_start: 0.2929 (OUTLIER) cc_final: 0.1734 (mmp)
REVERT: C  555 ASP cc_start: 0.3691 (OUTLIER) cc_final: 0.2784 (t0)
REVERT: C  671 ARG cc_start: 0.7196 (mtp-110) cc_final: 0.6773 (mmm160)
REVERT: C  676 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8042 (tpt90)
  outliers start: 98
  outliers final: 32
  residues processed: 208
  average time/residue: 1.0893
  time to fit residues: 246.6789
Evaluate side-chains
  156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 114
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  254 LYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  555 ASP
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  676 ARG
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  254 LYS
Chi-restraints excluded: chain C residue  258 TRP
Chi-restraints excluded: chain C residue  266 TYR
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain C residue  278 LYS
Chi-restraints excluded: chain C residue  281 CYS
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  508 MET
Chi-restraints excluded: chain C residue  510 ILE
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  555 ASP
Chi-restraints excluded: chain C residue  646 LEU
Chi-restraints excluded: chain C residue  676 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 124 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    0.4980
   chunk 80 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 69 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   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  63 ASN
A 575 GLN
A 616 GLN
C  63 ASN
C 575 GLN
C 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.190565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.120878 restraints weight = 11610.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.11
r_work: 0.3216 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11018  Z= 0.159
  Angle     :  0.704  16.741  14966  Z= 0.339
  Chirality :  0.044   0.177   1678
  Planarity :  0.005   0.039   1872
  Dihedral  :  7.223  59.254   1500
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.66 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  7.57 %
    Allowed  : 24.12 %
    Favored  : 68.31 %
  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: -0.51 (0.23), residues: 1316
  helix:  1.23 (0.18), residues: 850
  sheet: -3.68 (0.52), residues: 46
  loop : -3.40 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 625 
 HIS   0.004   0.001   HIS C 651 
 PHE   0.011   0.001   PHE C 548 
 TYR   0.007   0.001   TYR C 361 
 ARG   0.006   0.000   ARG C 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04618 (  664)
  hydrogen bonds       : angle       4.82466 ( 1944)
  covalent geometry    : bond        0.00349 (11018)
  covalent geometry    : angle       0.70395 (14966)

*********************** 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
  210 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 124
  time to evaluate  : 1.252 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.2401 (OUTLIER) cc_final: 0.0216 (t80)
REVERT: A  254 LYS cc_start: 0.5883 (OUTLIER) cc_final: 0.5570 (mttp)
REVERT: A  258 TRP cc_start: 0.4027 (OUTLIER) cc_final: 0.3218 (t60)
REVERT: A  278 LYS cc_start: 0.0406 (OUTLIER) cc_final: 0.0019 (ttmt)
REVERT: A  287 GLN cc_start: 0.5567 (OUTLIER) cc_final: 0.5006 (pm20)
REVERT: A  348 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8300 (mt-10)
REVERT: A  353 TRP cc_start: 0.8124 (m100) cc_final: 0.6991 (t60)
REVERT: A  555 ASP cc_start: 0.3262 (OUTLIER) cc_final: 0.2704 (t0)
REVERT: A  646 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5818 (tp)
REVERT: A  676 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7856 (tpt90)
REVERT: C   61 PHE cc_start: 0.2386 (OUTLIER) cc_final: 0.0210 (t80)
REVERT: C  254 LYS cc_start: 0.5896 (OUTLIER) cc_final: 0.5582 (mttp)
REVERT: C  258 TRP cc_start: 0.4024 (OUTLIER) cc_final: 0.3217 (t60)
REVERT: C  278 LYS cc_start: 0.0406 (OUTLIER) cc_final: 0.0015 (ttmt)
REVERT: C  287 GLN cc_start: 0.5560 (OUTLIER) cc_final: 0.4999 (pm20)
REVERT: C  348 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8302 (mt-10)
REVERT: C  353 TRP cc_start: 0.8119 (m100) cc_final: 0.6987 (t60)
REVERT: C  555 ASP cc_start: 0.3259 (OUTLIER) cc_final: 0.2702 (t0)
REVERT: C  646 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5836 (tp)
REVERT: C  676 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7862 (tpt90)
  outliers start: 86
  outliers final: 30
  residues processed: 202
  average time/residue: 1.2147
  time to fit residues: 266.5457
Evaluate side-chains
  158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 112
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  254 LYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  555 ASP
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  569 THR
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  676 ARG
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  232 ASN
Chi-restraints excluded: chain C residue  254 LYS
Chi-restraints excluded: chain C residue  258 TRP
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  266 TYR
Chi-restraints excluded: chain C residue  278 LYS
Chi-restraints excluded: chain C residue  281 CYS
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  510 ILE
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  555 ASP
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  569 THR
Chi-restraints excluded: chain C residue  646 LEU
Chi-restraints excluded: chain C residue  676 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 36 optimal weight:    8.9990
   chunk 103 optimal weight:   20.0000
   chunk 66 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
A 616 GLN
C 272 GLN
C 616 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.189416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.118830 restraints weight = 11411.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.10
r_work: 0.3210 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  11018  Z= 0.162
  Angle     :  0.664  14.380  14966  Z= 0.320
  Chirality :  0.044   0.143   1678
  Planarity :  0.005   0.041   1872
  Dihedral  :  6.886  55.526   1498
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.60 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 24.82 %
    Favored  : 68.66 %
  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 (0.23), residues: 1316
  helix:  1.22 (0.17), residues: 854
  sheet: -3.47 (0.55), residues: 46
  loop : -3.27 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 625 
 HIS   0.003   0.001   HIS C 651 
 PHE   0.010   0.001   PHE C 225 
 TYR   0.010   0.001   TYR A 361 
 ARG   0.005   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04297 (  664)
  hydrogen bonds       : angle       4.62215 ( 1944)
  covalent geometry    : bond        0.00360 (11018)
  covalent geometry    : angle       0.66377 (14966)

*********************** 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
  204 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 130
  time to evaluate  : 1.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.6885 (mm-40) cc_final: 0.6643 (mm-40)
REVERT: A   61 PHE cc_start: 0.2392 (OUTLIER) cc_final: 0.0272 (t80)
REVERT: A  278 LYS cc_start: 0.0356 (OUTLIER) cc_final: 0.0059 (ttmt)
REVERT: A  287 GLN cc_start: 0.5656 (OUTLIER) cc_final: 0.5075 (pm20)
REVERT: A  288 LYS cc_start: 0.3321 (OUTLIER) cc_final: 0.2757 (pptt)
REVERT: A  292 ILE cc_start: 0.0733 (OUTLIER) cc_final: 0.0090 (pp)
REVERT: A  348 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8263 (mt-10)
REVERT: A  353 TRP cc_start: 0.8144 (m100) cc_final: 0.6989 (t60)
REVERT: A  508 MET cc_start: 0.3276 (tpt) cc_final: 0.1995 (mmp)
REVERT: A  555 ASP cc_start: 0.3203 (OUTLIER) cc_final: 0.2783 (t0)
REVERT: A  646 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5956 (tp)
REVERT: A  676 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8164 (tpt90)
REVERT: A  711 ASP cc_start: 0.8371 (p0) cc_final: 0.7824 (m-30)
REVERT: C   31 GLN cc_start: 0.6910 (mm-40) cc_final: 0.6668 (mm-40)
REVERT: C   61 PHE cc_start: 0.2399 (OUTLIER) cc_final: 0.0271 (t80)
REVERT: C  278 LYS cc_start: 0.0357 (OUTLIER) cc_final: 0.0060 (ttmt)
REVERT: C  287 GLN cc_start: 0.5651 (OUTLIER) cc_final: 0.5072 (pm20)
REVERT: C  288 LYS cc_start: 0.3327 (OUTLIER) cc_final: 0.2763 (pptt)
REVERT: C  292 ILE cc_start: 0.0715 (OUTLIER) cc_final: 0.0078 (pp)
REVERT: C  348 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8268 (mt-10)
REVERT: C  353 TRP cc_start: 0.8137 (m100) cc_final: 0.6985 (t60)
REVERT: C  508 MET cc_start: 0.3268 (tpt) cc_final: 0.1984 (mmp)
REVERT: C  555 ASP cc_start: 0.3199 (OUTLIER) cc_final: 0.2779 (t0)
REVERT: C  646 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5974 (tp)
REVERT: C  676 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8160 (tpt90)
REVERT: C  711 ASP cc_start: 0.8364 (p0) cc_final: 0.7818 (m-30)
  outliers start: 74
  outliers final: 24
  residues processed: 190
  average time/residue: 1.7591
  time to fit residues: 359.4455
Evaluate side-chains
  156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 116
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  555 ASP
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  569 THR
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  676 ARG
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  232 ASN
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  266 TYR
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain C residue  278 LYS
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain C residue  288 LYS
Chi-restraints excluded: chain C residue  292 ILE
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  510 ILE
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  555 ASP
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  569 THR
Chi-restraints excluded: chain C residue  646 LEU
Chi-restraints excluded: chain C residue  676 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9990
   chunk 51 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 575 GLN
A 616 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 GLN
** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 575 GLN
C 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.189436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.118728 restraints weight = 11393.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.10
r_work: 0.3219 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11018  Z= 0.147
  Angle     :  0.634  12.422  14966  Z= 0.308
  Chirality :  0.043   0.162   1678
  Planarity :  0.005   0.041   1872
  Dihedral  :  6.543  56.021   1496
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 25.88 %
    Favored  : 67.96 %
  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: -0.29 (0.23), residues: 1316
  helix:  1.34 (0.18), residues: 854
  sheet: -3.39 (0.57), residues: 46
  loop : -3.23 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 625 
 HIS   0.003   0.001   HIS A 651 
 PHE   0.009   0.001   PHE C 225 
 TYR   0.009   0.001   TYR A 361 
 ARG   0.005   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04178 (  664)
  hydrogen bonds       : angle       4.49647 ( 1944)
  covalent geometry    : bond        0.00327 (11018)
  covalent geometry    : angle       0.63391 (14966)

*********************** 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
  188 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 118
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6596 (mm-40)
REVERT: A   61 PHE cc_start: 0.2382 (OUTLIER) cc_final: 0.0215 (t80)
REVERT: A  278 LYS cc_start: 0.0312 (OUTLIER) cc_final: 0.0018 (ttmt)
REVERT: A  287 GLN cc_start: 0.5662 (OUTLIER) cc_final: 0.5078 (pm20)
REVERT: A  288 LYS cc_start: 0.3188 (OUTLIER) cc_final: 0.2652 (pptt)
REVERT: A  348 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8233 (mt-10)
REVERT: A  508 MET cc_start: 0.3273 (tpt) cc_final: 0.2022 (mmp)
REVERT: A  555 ASP cc_start: 0.3207 (OUTLIER) cc_final: 0.2828 (t0)
REVERT: A  646 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.6023 (tp)
REVERT: A  676 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8124 (tpt90)
REVERT: A  711 ASP cc_start: 0.8359 (p0) cc_final: 0.7827 (m-30)
REVERT: C   31 GLN cc_start: 0.6872 (mm-40) cc_final: 0.6620 (mm-40)
REVERT: C   61 PHE cc_start: 0.2392 (OUTLIER) cc_final: 0.0216 (t80)
REVERT: C  278 LYS cc_start: 0.0314 (OUTLIER) cc_final: 0.0021 (ttmt)
REVERT: C  287 GLN cc_start: 0.5654 (OUTLIER) cc_final: 0.5074 (pm20)
REVERT: C  288 LYS cc_start: 0.3199 (OUTLIER) cc_final: 0.2664 (pptt)
REVERT: C  348 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8244 (mt-10)
REVERT: C  508 MET cc_start: 0.3266 (tpt) cc_final: 0.2013 (mmp)
REVERT: C  555 ASP cc_start: 0.3211 (OUTLIER) cc_final: 0.2828 (t0)
REVERT: C  646 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.6054 (tp)
REVERT: C  676 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8124 (tpt90)
REVERT: C  711 ASP cc_start: 0.8348 (p0) cc_final: 0.7819 (m-30)
  outliers start: 70
  outliers final: 28
  residues processed: 174
  average time/residue: 1.3986
  time to fit residues: 263.1827
Evaluate side-chains
  152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 110
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  522 MET
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  555 ASP
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  569 THR
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  676 ARG
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue   78 GLU
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  232 ASN
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  266 TYR
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain C residue  278 LYS
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain C residue  288 LYS
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  522 MET
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  555 ASP
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  569 THR
Chi-restraints excluded: chain C residue  613 VAL
Chi-restraints excluded: chain C residue  646 LEU
Chi-restraints excluded: chain C residue  676 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 98 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 112 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 124 optimal weight:    0.9980
   chunk 130 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
A 272 GLN
A 616 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 GLN
C 272 GLN
C 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.188748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.118731 restraints weight = 11470.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.08
r_work: 0.3198 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.5326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11018  Z= 0.149
  Angle     :  0.622  11.432  14966  Z= 0.304
  Chirality :  0.042   0.142   1678
  Planarity :  0.005   0.042   1872
  Dihedral  :  6.132  56.080   1492
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 26.06 %
    Favored  : 67.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.23), residues: 1316
  helix:  1.41 (0.18), residues: 854
  sheet: -3.32 (0.59), residues: 46
  loop : -3.11 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 625 
 HIS   0.003   0.001   HIS A 651 
 PHE   0.009   0.001   PHE C 225 
 TYR   0.009   0.001   TYR A 361 
 ARG   0.005   0.000   ARG C 671 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (  664)
  hydrogen bonds       : angle       4.43395 ( 1944)
  covalent geometry    : bond        0.00334 (11018)
  covalent geometry    : angle       0.62249 (14966)

*********************** 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
  200 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 126
  time to evaluate  : 1.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 LYS cc_start: 0.0357 (OUTLIER) cc_final: 0.0136 (ttmt)
REVERT: A  287 GLN cc_start: 0.5664 (OUTLIER) cc_final: 0.5156 (pm20)
REVERT: A  288 LYS cc_start: 0.3115 (OUTLIER) cc_final: 0.2677 (pptt)
REVERT: A  348 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8227 (mt-10)
REVERT: A  508 MET cc_start: 0.3384 (tpt) cc_final: 0.2051 (mmp)
REVERT: A  551 LYS cc_start: 0.4482 (OUTLIER) cc_final: 0.4274 (mmtt)
REVERT: A  555 ASP cc_start: 0.3160 (OUTLIER) cc_final: 0.2878 (t0)
REVERT: A  676 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8178 (tpt90)
REVERT: A  711 ASP cc_start: 0.8387 (p0) cc_final: 0.7866 (m-30)
REVERT: C  278 LYS cc_start: 0.0354 (OUTLIER) cc_final: 0.0135 (ttmt)
REVERT: C  287 GLN cc_start: 0.5653 (OUTLIER) cc_final: 0.5148 (pm20)
REVERT: C  288 LYS cc_start: 0.3113 (OUTLIER) cc_final: 0.2677 (pptt)
REVERT: C  348 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8220 (mt-10)
REVERT: C  508 MET cc_start: 0.3342 (tpt) cc_final: 0.2037 (mmp)
REVERT: C  551 LYS cc_start: 0.4480 (OUTLIER) cc_final: 0.4270 (mmtt)
REVERT: C  555 ASP cc_start: 0.3162 (OUTLIER) cc_final: 0.2880 (t0)
REVERT: C  676 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8158 (tpt90)
REVERT: C  711 ASP cc_start: 0.8373 (p0) cc_final: 0.7855 (m-30)
  outliers start: 74
  outliers final: 32
  residues processed: 186
  average time/residue: 1.4619
  time to fit residues: 293.6135
Evaluate side-chains
  158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 114
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  522 MET
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  555 ASP
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  569 THR
Chi-restraints excluded: chain A residue  676 ARG
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue   78 GLU
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  232 ASN
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  266 TYR
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain C residue  278 LYS
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain C residue  288 LYS
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  522 MET
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  551 LYS
Chi-restraints excluded: chain C residue  555 ASP
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  569 THR
Chi-restraints excluded: chain C residue  676 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 125 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 123 optimal weight:    0.5980
   chunk 37 optimal weight:   30.0000
   chunk 36 optimal weight:    9.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
A 575 GLN
A 616 GLN
C 190 GLN
C 575 GLN
C 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.188533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.118028 restraints weight = 11583.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.11
r_work: 0.3183 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.5404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11018  Z= 0.146
  Angle     :  0.651  17.353  14966  Z= 0.311
  Chirality :  0.043   0.211   1678
  Planarity :  0.005   0.041   1872
  Dihedral  :  6.063  56.454   1492
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 28.17 %
    Favored  : 67.08 %
  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: -0.10 (0.23), residues: 1316
  helix:  1.45 (0.18), residues: 856
  sheet: -3.36 (0.59), residues: 46
  loop : -3.06 (0.27), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 625 
 HIS   0.003   0.001   HIS A 651 
 PHE   0.009   0.001   PHE A 225 
 TYR   0.009   0.001   TYR A 361 
 ARG   0.006   0.000   ARG C 671 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04052 (  664)
  hydrogen bonds       : angle       4.36863 ( 1944)
  covalent geometry    : bond        0.00324 (11018)
  covalent geometry    : angle       0.65059 (14966)

*********************** 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
  176 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 122
  time to evaluate  : 1.275 
Fit side-chains
REVERT: A  278 LYS cc_start: 0.0364 (OUTLIER) cc_final: 0.0159 (ttmt)
REVERT: A  287 GLN cc_start: 0.5676 (OUTLIER) cc_final: 0.5178 (pm20)
REVERT: A  288 LYS cc_start: 0.3108 (OUTLIER) cc_final: 0.2648 (pptt)
REVERT: A  348 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8225 (mt-10)
REVERT: A  508 MET cc_start: 0.3358 (tpt) cc_final: 0.2064 (mmp)
REVERT: A  676 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8165 (tpt90)
REVERT: A  711 ASP cc_start: 0.8383 (p0) cc_final: 0.7865 (m-30)
REVERT: C  278 LYS cc_start: 0.0361 (OUTLIER) cc_final: 0.0157 (ttmt)
REVERT: C  287 GLN cc_start: 0.5670 (OUTLIER) cc_final: 0.5178 (pm20)
REVERT: C  288 LYS cc_start: 0.3121 (OUTLIER) cc_final: 0.2659 (pptt)
REVERT: C  348 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8222 (mt-10)
REVERT: C  508 MET cc_start: 0.3346 (tpt) cc_final: 0.2059 (mmp)
REVERT: C  676 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8152 (tpt90)
REVERT: C  711 ASP cc_start: 0.8379 (p0) cc_final: 0.7863 (m-30)
  outliers start: 54
  outliers final: 28
  residues processed: 164
  average time/residue: 1.3400
  time to fit residues: 237.4204
Evaluate side-chains
  152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 116
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  522 MET
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  569 THR
Chi-restraints excluded: chain A residue  676 ARG
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue   78 GLU
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  232 ASN
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  266 TYR
Chi-restraints excluded: chain C residue  278 LYS
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain C residue  288 LYS
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain C residue  522 MET
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  569 THR
Chi-restraints excluded: chain C residue  676 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 35 optimal weight:    0.1980
   chunk 3 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
A 272 GLN
A 616 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 GLN
C 272 GLN
C 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.187332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.117784 restraints weight = 11436.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.07
r_work: 0.3156 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.5549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11018  Z= 0.158
  Angle     :  0.642  15.331  14966  Z= 0.310
  Chirality :  0.043   0.175   1678
  Planarity :  0.005   0.042   1872
  Dihedral  :  5.988  56.039   1488
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 27.99 %
    Favored  : 67.78 %
  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 (0.23), residues: 1316
  helix:  1.42 (0.17), residues: 860
  sheet: -3.42 (0.58), residues: 46
  loop : -2.97 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 625 
 HIS   0.003   0.001   HIS A 651 
 PHE   0.011   0.001   PHE A  33 
 TYR   0.013   0.001   TYR C 577 
 ARG   0.006   0.000   ARG C 671 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04139 (  664)
  hydrogen bonds       : angle       4.34570 ( 1944)
  covalent geometry    : bond        0.00359 (11018)
  covalent geometry    : angle       0.64226 (14966)

*********************** 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
  172 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 124
  time to evaluate  : 2.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  287 GLN cc_start: 0.5644 (OUTLIER) cc_final: 0.5112 (pm20)
REVERT: A  288 LYS cc_start: 0.3076 (OUTLIER) cc_final: 0.2546 (pptt)
REVERT: A  348 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8081 (mt-10)
REVERT: A  551 LYS cc_start: 0.4481 (OUTLIER) cc_final: 0.4248 (mmtt)
REVERT: A  676 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8030 (tpt90)
REVERT: A  697 ARG cc_start: 0.6994 (mtt90) cc_final: 0.6727 (mtt90)
REVERT: A  711 ASP cc_start: 0.8299 (p0) cc_final: 0.7731 (m-30)
REVERT: C  287 GLN cc_start: 0.5637 (OUTLIER) cc_final: 0.5106 (pm20)
REVERT: C  288 LYS cc_start: 0.3076 (OUTLIER) cc_final: 0.2541 (pptt)
REVERT: C  348 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8074 (mt-10)
REVERT: C  551 LYS cc_start: 0.4483 (OUTLIER) cc_final: 0.4246 (mmtt)
REVERT: C  676 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7985 (tpt90)
REVERT: C  697 ARG cc_start: 0.7018 (mtt90) cc_final: 0.6750 (mtt90)
REVERT: C  711 ASP cc_start: 0.8297 (p0) cc_final: 0.7736 (m-30)
  outliers start: 48
  outliers final: 28
  residues processed: 166
  average time/residue: 1.3626
  time to fit residues: 245.1074
Evaluate side-chains
  158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  522 MET
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  569 THR
Chi-restraints excluded: chain A residue  676 ARG
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   78 GLU
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  232 ASN
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  266 TYR
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain C residue  288 LYS
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain C residue  522 MET
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  551 LYS
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  569 THR
Chi-restraints excluded: chain C residue  676 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 131 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   chunk 109 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
A 272 GLN
A 616 GLN
C 190 GLN
C 272 GLN
C 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.186870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.117496 restraints weight = 11655.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.09
r_work: 0.3157 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.5599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11018  Z= 0.162
  Angle     :  0.644  15.133  14966  Z= 0.311
  Chirality :  0.043   0.167   1678
  Planarity :  0.005   0.041   1872
  Dihedral  :  5.804  56.283   1476
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 28.17 %
    Favored  : 67.78 %
  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: -0.05 (0.23), residues: 1316
  helix:  1.43 (0.17), residues: 860
  sheet: -3.42 (0.58), residues: 46
  loop : -2.94 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 625 
 HIS   0.003   0.001   HIS A 651 
 PHE   0.010   0.001   PHE C 225 
 TYR   0.010   0.001   TYR A 361 
 ARG   0.007   0.000   ARG C 671 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04135 (  664)
  hydrogen bonds       : angle       4.33596 ( 1944)
  covalent geometry    : bond        0.00372 (11018)
  covalent geometry    : angle       0.64356 (14966)

*********************** 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
  170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 124
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 LYS cc_start: 0.5766 (OUTLIER) cc_final: 0.5172 (mttt)
REVERT: A  287 GLN cc_start: 0.5653 (OUTLIER) cc_final: 0.5124 (pm20)
REVERT: A  288 LYS cc_start: 0.3075 (OUTLIER) cc_final: 0.2533 (pptt)
REVERT: A  348 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8035 (mt-10)
REVERT: A  371 SER cc_start: 0.7885 (m) cc_final: 0.7416 (p)
REVERT: A  508 MET cc_start: 0.3334 (tpt) cc_final: 0.2082 (mmp)
REVERT: A  551 LYS cc_start: 0.4496 (OUTLIER) cc_final: 0.4249 (mmtt)
REVERT: A  676 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7970 (tpt90)
REVERT: A  711 ASP cc_start: 0.8267 (p0) cc_final: 0.7693 (m-30)
REVERT: C  254 LYS cc_start: 0.5784 (OUTLIER) cc_final: 0.5188 (mttt)
REVERT: C  287 GLN cc_start: 0.5645 (OUTLIER) cc_final: 0.5118 (pm20)
REVERT: C  288 LYS cc_start: 0.3074 (OUTLIER) cc_final: 0.2529 (pptt)
REVERT: C  348 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8027 (mt-10)
REVERT: C  371 SER cc_start: 0.7880 (m) cc_final: 0.7410 (p)
REVERT: C  508 MET cc_start: 0.3318 (tpt) cc_final: 0.2076 (mmp)
REVERT: C  551 LYS cc_start: 0.4497 (OUTLIER) cc_final: 0.4247 (mmtt)
REVERT: C  676 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7931 (tpt90)
REVERT: C  711 ASP cc_start: 0.8271 (p0) cc_final: 0.7701 (m-30)
  outliers start: 46
  outliers final: 30
  residues processed: 166
  average time/residue: 1.1575
  time to fit residues: 208.4593
Evaluate side-chains
  160 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 120
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  254 LYS
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  522 MET
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  569 THR
Chi-restraints excluded: chain A residue  676 ARG
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  232 ASN
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  254 LYS
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  266 TYR
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain C residue  288 LYS
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  522 MET
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  551 LYS
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  569 THR
Chi-restraints excluded: chain C residue  676 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 114 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 108 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
A 272 GLN
A 616 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 GLN
C 272 GLN
C 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.187223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.117851 restraints weight = 11566.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.09
r_work: 0.3153 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.5652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11018  Z= 0.154
  Angle     :  0.639  14.516  14966  Z= 0.310
  Chirality :  0.043   0.156   1678
  Planarity :  0.005   0.041   1872
  Dihedral  :  5.774  56.391   1476
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 28.52 %
    Favored  : 67.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.23), residues: 1316
  helix:  1.51 (0.17), residues: 856
  sheet: -3.45 (0.58), residues: 46
  loop : -2.95 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 625 
 HIS   0.003   0.001   HIS A 651 
 PHE   0.013   0.001   PHE C  27 
 TYR   0.010   0.001   TYR A 361 
 ARG   0.008   0.000   ARG C 671 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  664)
  hydrogen bonds       : angle       4.31264 ( 1944)
  covalent geometry    : bond        0.00348 (11018)
  covalent geometry    : angle       0.63943 (14966)

********************** 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
  172 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 126
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7591 (mmtt)
REVERT: A  254 LYS cc_start: 0.5782 (OUTLIER) cc_final: 0.5173 (mttt)
REVERT: A  287 GLN cc_start: 0.5636 (OUTLIER) cc_final: 0.5118 (pm20)
REVERT: A  288 LYS cc_start: 0.3072 (OUTLIER) cc_final: 0.2544 (pptt)
REVERT: A  348 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8062 (mt-10)
REVERT: A  371 SER cc_start: 0.7925 (m) cc_final: 0.7470 (p)
REVERT: A  508 MET cc_start: 0.3389 (tpt) cc_final: 0.2114 (mmp)
REVERT: A  551 LYS cc_start: 0.4536 (OUTLIER) cc_final: 0.4282 (mmtt)
REVERT: A  676 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8021 (tpt90)
REVERT: A  711 ASP cc_start: 0.8279 (p0) cc_final: 0.7742 (m-30)
REVERT: C  179 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7601 (mmtt)
REVERT: C  254 LYS cc_start: 0.5794 (OUTLIER) cc_final: 0.5181 (mttt)
REVERT: C  287 GLN cc_start: 0.5625 (OUTLIER) cc_final: 0.5107 (pm20)
REVERT: C  288 LYS cc_start: 0.3069 (OUTLIER) cc_final: 0.2539 (pptt)
REVERT: C  348 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8050 (mt-10)
REVERT: C  371 SER cc_start: 0.7926 (m) cc_final: 0.7471 (p)
REVERT: C  508 MET cc_start: 0.3398 (tpt) cc_final: 0.2114 (mmp)
REVERT: C  551 LYS cc_start: 0.4537 (OUTLIER) cc_final: 0.4281 (mmtt)
REVERT: C  676 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7982 (tpt90)
REVERT: C  711 ASP cc_start: 0.8287 (p0) cc_final: 0.7756 (m-30)
  outliers start: 46
  outliers final: 24
  residues processed: 168
  average time/residue: 1.7031
  time to fit residues: 311.6202
Evaluate side-chains
  158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 1.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  254 LYS
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  522 MET
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  551 LYS
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  676 ARG
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue  179 LYS
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  232 ASN
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  254 LYS
Chi-restraints excluded: chain C residue  259 LEU
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain C residue  287 GLN
Chi-restraints excluded: chain C residue  288 LYS
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain C residue  522 MET
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  551 LYS
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  676 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 129 optimal weight:    0.4980
   chunk 100 optimal weight:    0.8980
   chunk 85 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0670
   chunk 65 optimal weight:    0.1980
   chunk 121 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0980
   chunk 10 optimal weight:    0.8980
   chunk 128 optimal weight:    0.6980
   overall best weight:    0.2118

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
A 272 GLN
A 616 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 GLN
C 272 GLN
C 616 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.190269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.121779 restraints weight = 11444.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.07
r_work: 0.3219 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.5785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11018  Z= 0.123
  Angle     :  0.618  13.560  14966  Z= 0.298
  Chirality :  0.042   0.199   1678
  Planarity :  0.005   0.040   1872
  Dihedral  :  5.567  57.232   1476
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 29.40 %
    Favored  : 67.25 %
  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:  0.22 (0.24), residues: 1316
  helix:  1.67 (0.18), residues: 858
  sheet: -3.38 (0.59), residues: 46
  loop : -2.86 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 625 
 HIS   0.004   0.000   HIS A 651 
 PHE   0.009   0.001   PHE A  33 
 TYR   0.007   0.001   TYR C 713 
 ARG   0.008   0.000   ARG A 671 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03677 (  664)
  hydrogen bonds       : angle       4.19561 ( 1944)
  covalent geometry    : bond        0.00257 (11018)
  covalent geometry    : angle       0.61771 (14966)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14886.89 seconds
wall clock time: 268 minutes 51.57 seconds (16131.57 seconds total)