Starting phenix.real_space_refine
on Sat Oct 11 01:58:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ymo_39401/10_2025/8ymo_39401_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ymo_39401/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ymo_39401/10_2025/8ymo_39401_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ymo_39401/10_2025/8ymo_39401_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ymo_39401/10_2025/8ymo_39401.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ymo_39401/10_2025/8ymo_39401.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 4.79, per 1000 atoms: 0.45
  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: 1.03
  Conformation dependent library (CDL) restraints added in 444.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.35
  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: 1.81

  Time building geometry restraints manager: 1.33 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: 0.02
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:             31.540
  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:          0.820
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.540
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.970
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG C 331 
 TYR   0.010   0.001   TYR C 618 
 PHE   0.011   0.002   PHE C 383 
 TRP   0.017   0.002   TRP C 625 
 HIS   0.004   0.001   HIS C 651 

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

*********************** 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  : 0.460 
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: 0.5601
  time to fit residues: 302.1276
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  : 0.413 
-------------------------------------------------------------------------------
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 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  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 272 GLN
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: 35

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.190246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.119099 restraints weight = 11049.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.09
r_work: 0.3166 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.4069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  11018  Z= 0.205
  Angle     :  0.781  16.480  14966  Z= 0.390
  Chirality :  0.046   0.205   1678
  Planarity :  0.006   0.045   1872
  Dihedral  :  9.031  59.238   1542
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.05 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  9.51 %
    Allowed  : 24.12 %
    Favored  : 66.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.23), residues: 1316
  helix:  0.81 (0.17), residues: 850
  sheet: -3.78 (0.50), residues: 46
  loop : -3.58 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  60 
 TYR   0.024   0.002   TYR C  43 
 PHE   0.018   0.002   PHE A 438 
 TRP   0.026   0.002   TRP C 625 
 HIS   0.004   0.001   HIS C 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (11018)
  covalent geometry    : angle       0.78053 (14966)
  hydrogen bonds       : bond        0.05413 (  664)
  hydrogen bonds       : angle       5.35502 ( 1944)

*********************** 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
  226 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 108
    poor density    : 118
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 LYS cc_start: 0.0554 (OUTLIER) cc_final: -0.0003 (ttmt)
REVERT: A  318 LYS cc_start: 0.7986 (pttp) cc_final: 0.7769 (pmtt)
REVERT: A  353 TRP cc_start: 0.8277 (m100) cc_final: 0.7185 (t60)
REVERT: A  508 MET cc_start: 0.2932 (OUTLIER) cc_final: 0.1744 (mmp)
REVERT: A  555 ASP cc_start: 0.3661 (OUTLIER) cc_final: 0.2637 (t0)
REVERT: A  676 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7979 (tpt90)
REVERT: C  278 LYS cc_start: 0.0555 (OUTLIER) cc_final: -0.0001 (ttmt)
REVERT: C  318 LYS cc_start: 0.7986 (pttp) cc_final: 0.7772 (pmtt)
REVERT: C  353 TRP cc_start: 0.8271 (m100) cc_final: 0.7188 (t60)
REVERT: C  508 MET cc_start: 0.2956 (OUTLIER) cc_final: 0.1747 (mmp)
REVERT: C  555 ASP cc_start: 0.3661 (OUTLIER) cc_final: 0.2636 (t0)
REVERT: C  676 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7979 (tpt90)
  outliers start: 108
  outliers final: 34
  residues processed: 212
  average time/residue: 0.5602
  time to fit residues: 128.6950
Evaluate side-chains
  154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 112
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
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  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  565 ILE
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  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  565 ILE
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 55 optimal weight:    0.9990
   chunk 120 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 124 optimal weight:    0.6980
   chunk 45 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 263 GLN
A 616 GLN
C  63 ASN
C 616 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.189414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.119524 restraints weight = 11578.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.11
r_work: 0.3215 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.4595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11018  Z= 0.170
  Angle     :  0.708  15.384  14966  Z= 0.344
  Chirality :  0.045   0.219   1678
  Planarity :  0.005   0.040   1872
  Dihedral  :  7.233  57.627   1500
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.66 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 24.03 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.23), residues: 1316
  helix:  1.19 (0.18), residues: 854
  sheet: -3.61 (0.53), residues: 46
  loop : -3.45 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 376 
 TYR   0.008   0.001   TYR C 361 
 PHE   0.011   0.001   PHE C 548 
 TRP   0.021   0.001   TRP C 625 
 HIS   0.004   0.001   HIS C 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (11018)
  covalent geometry    : angle       0.70788 (14966)
  hydrogen bonds       : bond        0.04709 (  664)
  hydrogen bonds       : angle       4.84361 ( 1944)

*********************** 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
  192 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 116
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.2355 (OUTLIER) cc_final: 0.0210 (t80)
REVERT: A   78 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7369 (mt-10)
REVERT: A  254 LYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5509 (mttp)
REVERT: A  278 LYS cc_start: 0.0440 (OUTLIER) cc_final: 0.0034 (ttmt)
REVERT: A  287 GLN cc_start: 0.5577 (OUTLIER) cc_final: 0.5012 (pm20)
REVERT: A  348 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8228 (mt-10)
REVERT: A  353 TRP cc_start: 0.8161 (m100) cc_final: 0.6993 (t60)
REVERT: A  555 ASP cc_start: 0.3185 (OUTLIER) cc_final: 0.2645 (t0)
REVERT: A  646 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5773 (tp)
REVERT: C   61 PHE cc_start: 0.2352 (OUTLIER) cc_final: 0.0209 (t80)
REVERT: C   78 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7381 (mt-10)
REVERT: C  254 LYS cc_start: 0.5876 (OUTLIER) cc_final: 0.5547 (mttp)
REVERT: C  278 LYS cc_start: 0.0438 (OUTLIER) cc_final: 0.0049 (ttmt)
REVERT: C  287 GLN cc_start: 0.5584 (OUTLIER) cc_final: 0.5044 (pm20)
REVERT: C  348 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8235 (mt-10)
REVERT: C  353 TRP cc_start: 0.8145 (m100) cc_final: 0.6981 (t60)
REVERT: C  555 ASP cc_start: 0.3175 (OUTLIER) cc_final: 0.2635 (t0)
REVERT: C  646 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5798 (tp)
  outliers start: 76
  outliers final: 30
  residues processed: 186
  average time/residue: 0.5318
  time to fit residues: 107.1379
Evaluate side-chains
  154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 112
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
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  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  646 LEU
Chi-restraints excluded: chain A residue  705 LEU
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  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  646 LEU
Chi-restraints excluded: chain C residue  705 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 121 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
A 263 GLN
A 272 GLN
A 616 GLN
C 190 GLN
C 272 GLN
C 616 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.184953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.115188 restraints weight = 11585.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.07
r_work: 0.3143 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11018  Z= 0.225
  Angle     :  0.702  14.171  14966  Z= 0.343
  Chirality :  0.046   0.156   1678
  Planarity :  0.006   0.043   1872
  Dihedral  :  6.659  49.933   1490
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.83 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 24.21 %
    Favored  : 69.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.23), residues: 1316
  helix:  1.08 (0.17), residues: 856
  sheet: -3.03 (0.64), residues: 46
  loop : -3.27 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 376 
 TYR   0.014   0.002   TYR C 361 
 PHE   0.011   0.002   PHE C 225 
 TRP   0.019   0.002   TRP C 625 
 HIS   0.003   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (11018)
  covalent geometry    : angle       0.70232 (14966)
  hydrogen bonds       : bond        0.04894 (  664)
  hydrogen bonds       : angle       4.76830 ( 1944)

*********************** 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
  199 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 122
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.6976 (mm-40) cc_final: 0.6756 (mm-40)
REVERT: A   61 PHE cc_start: 0.2357 (OUTLIER) cc_final: 0.0253 (t80)
REVERT: A  254 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5641 (mttp)
REVERT: A  258 TRP cc_start: 0.4398 (OUTLIER) cc_final: 0.3072 (t60)
REVERT: A  278 LYS cc_start: 0.0331 (OUTLIER) cc_final: -0.0014 (ttmt)
REVERT: A  287 GLN cc_start: 0.5673 (OUTLIER) cc_final: 0.5101 (pm20)
REVERT: A  288 LYS cc_start: 0.3456 (OUTLIER) cc_final: 0.2881 (pptt)
REVERT: A  292 ILE cc_start: 0.0725 (OUTLIER) cc_final: 0.0086 (pp)
REVERT: A  296 ILE cc_start: 0.6182 (OUTLIER) cc_final: 0.5963 (mt)
REVERT: A  348 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8219 (mt-10)
REVERT: A  353 TRP cc_start: 0.8255 (m100) cc_final: 0.7070 (t60)
REVERT: A  508 MET cc_start: 0.3259 (tpt) cc_final: 0.1998 (mmp)
REVERT: A  555 ASP cc_start: 0.3129 (OUTLIER) cc_final: 0.2686 (t0)
REVERT: A  646 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5912 (tp)
REVERT: C   31 GLN cc_start: 0.6978 (mm-40) cc_final: 0.6759 (mm-40)
REVERT: C   61 PHE cc_start: 0.2371 (OUTLIER) cc_final: 0.0255 (t80)
REVERT: C  254 LYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5627 (mttp)
REVERT: C  258 TRP cc_start: 0.4397 (OUTLIER) cc_final: 0.3069 (t60)
REVERT: C  278 LYS cc_start: 0.0324 (OUTLIER) cc_final: -0.0014 (ttmt)
REVERT: C  287 GLN cc_start: 0.5641 (OUTLIER) cc_final: 0.5059 (pm20)
REVERT: C  288 LYS cc_start: 0.3383 (OUTLIER) cc_final: 0.2863 (pptt)
REVERT: C  292 ILE cc_start: 0.0780 (OUTLIER) cc_final: 0.0149 (pp)
REVERT: C  296 ILE cc_start: 0.6182 (OUTLIER) cc_final: 0.5966 (mt)
REVERT: C  348 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8217 (mt-10)
REVERT: C  353 TRP cc_start: 0.8240 (m100) cc_final: 0.7055 (t60)
REVERT: C  508 MET cc_start: 0.3249 (tpt) cc_final: 0.1984 (mmp)
REVERT: C  555 ASP cc_start: 0.3113 (OUTLIER) cc_final: 0.2675 (t0)
REVERT: C  646 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5915 (tp)
  outliers start: 77
  outliers final: 33
  residues processed: 187
  average time/residue: 0.5516
  time to fit residues: 111.7648
Evaluate side-chains
  169 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 116
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   74 HIS
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  287 GLN
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  535 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  591 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   74 HIS
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  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  296 ILE
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  510 ILE
Chi-restraints excluded: chain C residue  535 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  591 LEU
Chi-restraints excluded: chain C residue  646 LEU
Chi-restraints excluded: chain C residue  705 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 119 optimal weight:    0.1980
   chunk 128 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 98 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
A 546 ASN
A 616 GLN
C 546 ASN
C 616 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.187477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.116968 restraints weight = 11478.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.09
r_work: 0.3173 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.5131

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= 0.158
  Angle     :  0.645  12.787  14966  Z= 0.314
  Chirality :  0.043   0.167   1678
  Planarity :  0.005   0.043   1872
  Dihedral  :  6.136  46.522   1488
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 26.23 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.23), residues: 1316
  helix:  1.26 (0.18), residues: 854
  sheet: -3.42 (0.59), residues: 42
  loop : -3.14 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 376 
 TYR   0.010   0.001   TYR A 361 
 PHE   0.010   0.001   PHE A 225 
 TRP   0.021   0.001   TRP A 625 
 HIS   0.003   0.001   HIS A 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (11018)
  covalent geometry    : angle       0.64526 (14966)
  hydrogen bonds       : bond        0.04334 (  664)
  hydrogen bonds       : angle       4.54295 ( 1944)

*********************** 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
  192 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 130
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.6933 (mm-40) cc_final: 0.6679 (mm-40)
REVERT: A   61 PHE cc_start: 0.2345 (OUTLIER) cc_final: 0.0222 (t80)
REVERT: A  179 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7810 (mmtt)
REVERT: A  278 LYS cc_start: 0.0346 (OUTLIER) cc_final: 0.0023 (ttmt)
REVERT: A  287 GLN cc_start: 0.5660 (OUTLIER) cc_final: 0.5106 (pm20)
REVERT: A  288 LYS cc_start: 0.3256 (OUTLIER) cc_final: 0.2777 (pptt)
REVERT: A  292 ILE cc_start: 0.0698 (OUTLIER) cc_final: 0.0046 (pp)
REVERT: A  296 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5958 (mt)
REVERT: A  348 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8178 (mt-10)
REVERT: A  353 TRP cc_start: 0.8212 (m100) cc_final: 0.7040 (t60)
REVERT: A  508 MET cc_start: 0.3319 (tpt) cc_final: 0.2044 (mmp)
REVERT: A  551 LYS cc_start: 0.4471 (OUTLIER) cc_final: 0.4233 (mmtt)
REVERT: A  555 ASP cc_start: 0.3192 (OUTLIER) cc_final: 0.2814 (t0)
REVERT: A  646 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5982 (tp)
REVERT: C   31 GLN cc_start: 0.6957 (mm-40) cc_final: 0.6705 (mm-40)
REVERT: C   61 PHE cc_start: 0.2361 (OUTLIER) cc_final: 0.0224 (t80)
REVERT: C  179 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7821 (mmtt)
REVERT: C  278 LYS cc_start: 0.0351 (OUTLIER) cc_final: 0.0038 (ttmt)
REVERT: C  287 GLN cc_start: 0.5665 (OUTLIER) cc_final: 0.5132 (pm20)
REVERT: C  292 ILE cc_start: 0.0776 (OUTLIER) cc_final: 0.0129 (pp)
REVERT: C  296 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.5969 (mt)
REVERT: C  348 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8189 (mt-10)
REVERT: C  353 TRP cc_start: 0.8203 (m100) cc_final: 0.7033 (t60)
REVERT: C  508 MET cc_start: 0.3289 (tpt) cc_final: 0.2030 (mmp)
REVERT: C  551 LYS cc_start: 0.4473 (OUTLIER) cc_final: 0.4234 (mmtt)
REVERT: C  555 ASP cc_start: 0.3186 (OUTLIER) cc_final: 0.2809 (t0)
REVERT: C  646 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.6007 (tp)
  outliers start: 62
  outliers final: 28
  residues processed: 186
  average time/residue: 0.5771
  time to fit residues: 116.2626
Evaluate side-chains
  165 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 118
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  112 ILE
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  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  292 ILE
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  397 VAL
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  646 LEU
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  112 ILE
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  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  292 ILE
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain C residue  397 VAL
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  646 LEU
Chi-restraints excluded: chain C residue  705 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 24 optimal weight:   20.0000
   chunk 101 optimal weight:    1.9990
   chunk 108 optimal weight:    0.1980
   chunk 118 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 272 GLN
A 616 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 616 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.187124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.116920 restraints weight = 11497.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.07
r_work: 0.3153 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.5275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  11018  Z= 0.167
  Angle     :  0.641  11.978  14966  Z= 0.312
  Chirality :  0.043   0.157   1678
  Planarity :  0.005   0.043   1872
  Dihedral  :  5.780  46.995   1484
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 26.14 %
    Favored  : 67.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.23), residues: 1316
  helix:  1.29 (0.17), residues: 858
  sheet: -3.42 (0.60), residues: 42
  loop : -3.04 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 671 
 TYR   0.010   0.001   TYR C 361 
 PHE   0.010   0.001   PHE C 225 
 TRP   0.020   0.001   TRP A 625 
 HIS   0.003   0.001   HIS A 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (11018)
  covalent geometry    : angle       0.64057 (14966)
  hydrogen bonds       : bond        0.04305 (  664)
  hydrogen bonds       : angle       4.50759 ( 1944)

*********************** 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
  194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 126
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6691 (mm110)
REVERT: A   61 PHE cc_start: 0.2345 (OUTLIER) cc_final: 0.0205 (t80)
REVERT: A  179 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7806 (mmtt)
REVERT: A  278 LYS cc_start: 0.0357 (OUTLIER) cc_final: 0.0039 (ttmt)
REVERT: A  287 GLN cc_start: 0.5678 (OUTLIER) cc_final: 0.5123 (pm20)
REVERT: A  288 LYS cc_start: 0.3227 (OUTLIER) cc_final: 0.2749 (pptt)
REVERT: A  292 ILE cc_start: 0.0744 (OUTLIER) cc_final: 0.0126 (tt)
REVERT: A  348 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8169 (mt-10)
REVERT: A  353 TRP cc_start: 0.8207 (m100) cc_final: 0.7030 (t60)
REVERT: A  508 MET cc_start: 0.3381 (tpt) cc_final: 0.2036 (mmp)
REVERT: A  551 LYS cc_start: 0.4476 (OUTLIER) cc_final: 0.4235 (mmtt)
REVERT: A  555 ASP cc_start: 0.3214 (OUTLIER) cc_final: 0.2896 (t0)
REVERT: A  646 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6094 (tp)
REVERT: C   31 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6704 (mm110)
REVERT: C   61 PHE cc_start: 0.2349 (OUTLIER) cc_final: 0.0204 (t80)
REVERT: C  179 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7819 (mmtt)
REVERT: C  278 LYS cc_start: 0.0329 (OUTLIER) cc_final: 0.0023 (ttmt)
REVERT: C  287 GLN cc_start: 0.5658 (OUTLIER) cc_final: 0.5120 (pm20)
REVERT: C  288 LYS cc_start: 0.3188 (OUTLIER) cc_final: 0.2672 (pptt)
REVERT: C  292 ILE cc_start: 0.0737 (OUTLIER) cc_final: 0.0131 (tt)
REVERT: C  348 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8171 (mt-10)
REVERT: C  353 TRP cc_start: 0.8194 (m100) cc_final: 0.7013 (t60)
REVERT: C  508 MET cc_start: 0.3366 (tpt) cc_final: 0.2020 (mmp)
REVERT: C  551 LYS cc_start: 0.4475 (OUTLIER) cc_final: 0.4233 (mmtt)
REVERT: C  555 ASP cc_start: 0.3218 (OUTLIER) cc_final: 0.2901 (t0)
REVERT: C  646 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.6118 (tp)
  outliers start: 68
  outliers final: 34
  residues processed: 190
  average time/residue: 0.5423
  time to fit residues: 111.5419
Evaluate side-chains
  170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 118
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 SER
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  112 ILE
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  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  292 ILE
Chi-restraints excluded: chain A residue  301 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  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  646 LEU
Chi-restraints excluded: chain A residue  705 LEU
Chi-restraints excluded: chain C residue   49 SER
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  112 ILE
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  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  292 ILE
Chi-restraints excluded: chain C residue  301 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  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  646 LEU
Chi-restraints excluded: chain C residue  705 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 131 optimal weight:    0.0870
   chunk 18 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 128 optimal weight:    0.8980
   chunk 36 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 103 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   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  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 616 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 616 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.188791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118351 restraints weight = 11451.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.10
r_work: 0.3212 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.5400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11018  Z= 0.139
  Angle     :  0.649  16.997  14966  Z= 0.310
  Chirality :  0.043   0.205   1678
  Planarity :  0.005   0.042   1872
  Dihedral  :  5.559  45.193   1484
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 27.20 %
    Favored  : 67.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.24), residues: 1316
  helix:  1.43 (0.18), residues: 858
  sheet: -3.44 (0.60), residues: 42
  loop : -2.98 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 671 
 TYR   0.008   0.001   TYR C 361 
 PHE   0.009   0.001   PHE A  72 
 TRP   0.020   0.001   TRP A 625 
 HIS   0.003   0.001   HIS A 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11018)
  covalent geometry    : angle       0.64913 (14966)
  hydrogen bonds       : bond        0.04057 (  664)
  hydrogen bonds       : angle       4.38696 ( 1944)

*********************** 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
  181 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 125
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6643 (mm110)
REVERT: A   61 PHE cc_start: 0.2322 (OUTLIER) cc_final: 0.0266 (t80)
REVERT: A  254 LYS cc_start: 0.5765 (OUTLIER) cc_final: 0.5191 (mttt)
REVERT: A  278 LYS cc_start: 0.0376 (OUTLIER) cc_final: 0.0112 (ttmt)
REVERT: A  287 GLN cc_start: 0.5675 (OUTLIER) cc_final: 0.5120 (pm20)
REVERT: A  288 LYS cc_start: 0.3137 (OUTLIER) cc_final: 0.2662 (pptt)
REVERT: A  348 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8144 (mt-10)
REVERT: A  508 MET cc_start: 0.3417 (tpt) cc_final: 0.2077 (mmp)
REVERT: A  551 LYS cc_start: 0.4474 (OUTLIER) cc_final: 0.4230 (mmtt)
REVERT: A  711 ASP cc_start: 0.8359 (p0) cc_final: 0.7789 (m-30)
REVERT: C   31 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6650 (mm110)
REVERT: C   61 PHE cc_start: 0.2324 (OUTLIER) cc_final: 0.0265 (t80)
REVERT: C  254 LYS cc_start: 0.5790 (OUTLIER) cc_final: 0.5213 (mttt)
REVERT: C  278 LYS cc_start: 0.0341 (OUTLIER) cc_final: 0.0097 (ttmt)
REVERT: C  287 GLN cc_start: 0.5672 (OUTLIER) cc_final: 0.5135 (pm20)
REVERT: C  288 LYS cc_start: 0.3141 (OUTLIER) cc_final: 0.2622 (pptt)
REVERT: C  348 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8151 (mt-10)
REVERT: C  508 MET cc_start: 0.3406 (tpt) cc_final: 0.2065 (mmp)
REVERT: C  551 LYS cc_start: 0.4473 (OUTLIER) cc_final: 0.4232 (mmtt)
REVERT: C  711 ASP cc_start: 0.8352 (p0) cc_final: 0.7783 (m-30)
  outliers start: 56
  outliers final: 28
  residues processed: 177
  average time/residue: 0.5368
  time to fit residues: 102.9855
Evaluate side-chains
  158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 118
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  206 VAL
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  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  397 VAL
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  705 LEU
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   74 HIS
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  206 VAL
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  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  397 VAL
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  705 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 124 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 122 optimal weight:    0.2980
   chunk 125 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 272 GLN
A 616 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 616 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.188550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118357 restraints weight = 11405.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.09
r_work: 0.3152 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.5539

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= 0.143
  Angle     :  0.637  15.374  14966  Z= 0.306
  Chirality :  0.043   0.181   1678
  Planarity :  0.005   0.042   1872
  Dihedral  :  5.371  45.564   1480
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 27.64 %
    Favored  : 68.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.24), residues: 1316
  helix:  1.47 (0.17), residues: 860
  sheet: -3.45 (0.61), residues: 42
  loop : -2.93 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 671 
 TYR   0.007   0.001   TYR C 577 
 PHE   0.010   0.001   PHE C  33 
 TRP   0.019   0.001   TRP A 625 
 HIS   0.003   0.001   HIS A 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (11018)
  covalent geometry    : angle       0.63650 (14966)
  hydrogen bonds       : bond        0.04018 (  664)
  hydrogen bonds       : angle       4.34274 ( 1944)

*********************** 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
  175 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 128
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.6949 (mm-40) cc_final: 0.6728 (mm110)
REVERT: A   61 PHE cc_start: 0.2396 (OUTLIER) cc_final: 0.0309 (t80)
REVERT: A  179 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7943 (mmtt)
REVERT: A  254 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5335 (mttt)
REVERT: A  287 GLN cc_start: 0.5688 (OUTLIER) cc_final: 0.5160 (pm20)
REVERT: A  348 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8243 (mt-10)
REVERT: A  371 SER cc_start: 0.8161 (m) cc_final: 0.7767 (p)
REVERT: A  390 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7191 (t80)
REVERT: A  508 MET cc_start: 0.3511 (tpt) cc_final: 0.2189 (mmp)
REVERT: A  551 LYS cc_start: 0.4482 (OUTLIER) cc_final: 0.4236 (mmtt)
REVERT: A  711 ASP cc_start: 0.8412 (p0) cc_final: 0.7861 (m-30)
REVERT: C   31 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6721 (mm110)
REVERT: C   61 PHE cc_start: 0.2392 (OUTLIER) cc_final: 0.0306 (t80)
REVERT: C  179 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7946 (mmtt)
REVERT: C  254 LYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5348 (mttt)
REVERT: C  278 LYS cc_start: 0.0328 (OUTLIER) cc_final: 0.0123 (ttmt)
REVERT: C  287 GLN cc_start: 0.5643 (OUTLIER) cc_final: 0.5113 (pm20)
REVERT: C  288 LYS cc_start: 0.3020 (OUTLIER) cc_final: 0.2483 (pptt)
REVERT: C  348 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8235 (mt-10)
REVERT: C  371 SER cc_start: 0.8153 (m) cc_final: 0.7759 (p)
REVERT: C  390 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7190 (t80)
REVERT: C  508 MET cc_start: 0.3528 (tpt) cc_final: 0.2189 (mmp)
REVERT: C  551 LYS cc_start: 0.4499 (OUTLIER) cc_final: 0.4254 (mmtt)
REVERT: C  711 ASP cc_start: 0.8400 (p0) cc_final: 0.7853 (m-30)
  outliers start: 47
  outliers final: 23
  residues processed: 175
  average time/residue: 0.5737
  time to fit residues: 108.8726
Evaluate side-chains
  161 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 124
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  112 ILE
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  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  381 VAL
Chi-restraints excluded: chain A residue  390 PHE
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  705 LEU
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue  112 ILE
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  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  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  390 PHE
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  705 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 9 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9980
   chunk 131 optimal weight:    0.0970
   chunk 81 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 120 optimal weight:    0.7980
   chunk 127 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 616 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 616 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.188913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.120013 restraints weight = 11498.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.08
r_work: 0.3206 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.5626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11018  Z= 0.132
  Angle     :  0.631  15.023  14966  Z= 0.303
  Chirality :  0.043   0.174   1678
  Planarity :  0.005   0.041   1872
  Dihedral  :  5.147  44.616   1472
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 28.26 %
    Favored  : 68.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.24), residues: 1316
  helix:  1.53 (0.18), residues: 860
  sheet: -3.44 (0.62), residues: 42
  loop : -2.90 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 671 
 TYR   0.007   0.001   TYR A 713 
 PHE   0.009   0.001   PHE A  72 
 TRP   0.020   0.001   TRP A 625 
 HIS   0.003   0.001   HIS A 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (11018)
  covalent geometry    : angle       0.63053 (14966)
  hydrogen bonds       : bond        0.03895 (  664)
  hydrogen bonds       : angle       4.27693 ( 1944)

*********************** 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
  162 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  179 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7523 (mmtt)
REVERT: A  254 LYS cc_start: 0.5699 (OUTLIER) cc_final: 0.5112 (mttt)
REVERT: A  287 GLN cc_start: 0.5689 (OUTLIER) cc_final: 0.5238 (pm20)
REVERT: A  348 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7983 (mt-10)
REVERT: A  371 SER cc_start: 0.7836 (m) cc_final: 0.7422 (p)
REVERT: A  508 MET cc_start: 0.3380 (tpt) cc_final: 0.2154 (mmp)
REVERT: A  711 ASP cc_start: 0.8265 (p0) cc_final: 0.7690 (m-30)
REVERT: C  179 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7525 (mmtt)
REVERT: C  254 LYS cc_start: 0.5702 (OUTLIER) cc_final: 0.5115 (mttt)
REVERT: C  287 GLN cc_start: 0.5637 (OUTLIER) cc_final: 0.5114 (pm20)
REVERT: C  288 LYS cc_start: 0.3078 (OUTLIER) cc_final: 0.2525 (pptt)
REVERT: C  348 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7988 (mt-10)
REVERT: C  371 SER cc_start: 0.7843 (m) cc_final: 0.7427 (p)
REVERT: C  508 MET cc_start: 0.3388 (tpt) cc_final: 0.2150 (mmp)
REVERT: C  551 LYS cc_start: 0.4537 (OUTLIER) cc_final: 0.4282 (mmtt)
REVERT: C  711 ASP cc_start: 0.8271 (p0) cc_final: 0.7698 (m-30)
  outliers start: 33
  outliers final: 14
  residues processed: 160
  average time/residue: 0.5872
  time to fit residues: 101.6153
Evaluate side-chains
  149 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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  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  287 GLN
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  565 ILE
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  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  549 LEU
Chi-restraints excluded: chain C residue  551 LYS
Chi-restraints excluded: chain C residue  565 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   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  31 GLN
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 272 GLN
A 616 GLN
C  31 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4086 r_free = 0.4086 target = 0.187425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.118310 restraints weight = 11470.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.07
r_work: 0.3141 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.5726

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= 0.151
  Angle     :  0.635  14.089  14966  Z= 0.308
  Chirality :  0.043   0.160   1678
  Planarity :  0.005   0.041   1872
  Dihedral  :  5.152  47.256   1468
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 28.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.24), residues: 1316
  helix:  1.52 (0.17), residues: 860
  sheet: -3.43 (0.62), residues: 42
  loop : -2.88 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 671 
 TYR   0.009   0.001   TYR C 577 
 PHE   0.010   0.001   PHE A  72 
 TRP   0.017   0.001   TRP A 625 
 HIS   0.003   0.001   HIS A 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11018)
  covalent geometry    : angle       0.63453 (14966)
  hydrogen bonds       : bond        0.04089 (  664)
  hydrogen bonds       : angle       4.31750 ( 1944)

********************** 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
  163 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: A  179 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7549 (mmtt)
REVERT: A  254 LYS cc_start: 0.5768 (OUTLIER) cc_final: 0.5152 (mttt)
REVERT: A  287 GLN cc_start: 0.5678 (OUTLIER) cc_final: 0.5190 (pm20)
REVERT: A  348 GLU cc_start: 0.8224 (mt-10) cc_final: 0.8012 (mt-10)
REVERT: A  371 SER cc_start: 0.7856 (m) cc_final: 0.7420 (p)
REVERT: A  390 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.7047 (t80)
REVERT: A  508 MET cc_start: 0.3456 (tpt) cc_final: 0.2133 (mmp)
REVERT: A  697 ARG cc_start: 0.6976 (mtt90) cc_final: 0.6761 (mtt90)
REVERT: A  711 ASP cc_start: 0.8236 (p0) cc_final: 0.7693 (m-30)
REVERT: C  179 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7541 (mmtt)
REVERT: C  254 LYS cc_start: 0.5799 (OUTLIER) cc_final: 0.5221 (mttt)
REVERT: C  258 TRP cc_start: 0.4820 (OUTLIER) cc_final: 0.3969 (t60)
REVERT: C  287 GLN cc_start: 0.5590 (OUTLIER) cc_final: 0.5092 (pm20)
REVERT: C  288 LYS cc_start: 0.2953 (OUTLIER) cc_final: 0.2391 (pptt)
REVERT: C  348 GLU cc_start: 0.8219 (mt-10) cc_final: 0.8008 (mt-10)
REVERT: C  371 SER cc_start: 0.7872 (m) cc_final: 0.7434 (p)
REVERT: C  390 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.7050 (t80)
REVERT: C  508 MET cc_start: 0.3491 (tpt) cc_final: 0.2136 (mmp)
REVERT: C  697 ARG cc_start: 0.7007 (mtt90) cc_final: 0.6791 (mtt90)
REVERT: C  711 ASP cc_start: 0.8254 (p0) cc_final: 0.7705 (m-30)
  outliers start: 34
  outliers final: 19
  residues processed: 159
  average time/residue: 0.5282
  time to fit residues: 91.0238
Evaluate side-chains
  151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
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  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  313 VAL
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  565 ILE
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  238 VAL
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  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  390 PHE
Chi-restraints excluded: chain C residue  549 LEU
Chi-restraints excluded: chain C residue  565 ILE
Chi-restraints excluded: chain C residue  705 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 116 optimal weight:    0.0070
   chunk 108 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 110 optimal weight:    8.9990
   chunk 112 optimal weight:    0.8980
   chunk 102 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   overall best weight:    0.9400

-------------------------------------------------------------------------------
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 272 GLN
A 616 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 616 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.187157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.118153 restraints weight = 11539.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.08
r_work: 0.3148 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.5763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  11018  Z= 0.154
  Angle     :  0.633  13.671  14966  Z= 0.306
  Chirality :  0.043   0.157   1678
  Planarity :  0.005   0.041   1872
  Dihedral  :  5.132  47.042   1468
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 28.08 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.24), residues: 1316
  helix:  1.52 (0.17), residues: 860
  sheet: -3.42 (0.62), residues: 42
  loop : -2.85 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 671 
 TYR   0.007   0.001   TYR C 361 
 PHE   0.012   0.001   PHE C  27 
 TRP   0.018   0.001   TRP C 625 
 HIS   0.003   0.001   HIS A 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (11018)
  covalent geometry    : angle       0.63314 (14966)
  hydrogen bonds       : bond        0.04061 (  664)
  hydrogen bonds       : angle       4.30762 ( 1944)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6199.92 seconds
wall clock time: 106 minutes 13.19 seconds (6373.19 seconds total)