Starting phenix.real_space_refine
on Wed Sep 17 06:32:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gnr_51478/09_2025/9gnr_51478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gnr_51478/09_2025/9gnr_51478.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gnr_51478/09_2025/9gnr_51478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gnr_51478/09_2025/9gnr_51478.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gnr_51478/09_2025/9gnr_51478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gnr_51478/09_2025/9gnr_51478.cif"
  }
  resolution = 2.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.028
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: 6
    Type Number    sf(0)   Gaussians
     Ni      2      6.56       5
     P       1      5.49       5
     S      30      5.16       5
     C    3788      2.51       5
     N    1048      2.21       5
     O    1185      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6054
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 777
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'CXM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 952
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 117}
    Chain: "C"
      Number of atoms: 4318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4318
          Classifications: {'peptide': 570}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 541}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'KCX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 7
          Unusual residues: {' NI': 2, '2PA': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 27
    residue:
      pdb=" N   LYS A   8 " occ=0.70
      ... (7 atoms not shown)
      pdb=" NZ  LYS A   8 " occ=0.70
    residue:
      pdb=" N   GLN A  12 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NE2 GLN A  12 " occ=0.50
    residue:
      pdb=" N   LYS A  29 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ  LYS A  29 " occ=0.50
    residue:
      pdb=" N   MET A  44 " occ=0.70
      ... (6 atoms not shown)
      pdb=" CE  MET A  44 " occ=0.70
    residue:
      pdb=" N   MET A  70 " occ=0.70
      ... (6 atoms not shown)
      pdb=" CE  MET A  70 " occ=0.70
    residue:
      pdb=" N   ARG B  13 " occ=0.70
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  13 " occ=0.70
    residue:
      pdb=" N   GLY B  17 " occ=0.50
      ... (2 atoms not shown)
      pdb=" O   GLY B  17 " occ=0.50
    residue:
      pdb=" N   SER B  33 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER B  33 " occ=0.50
    residue:
      pdb=" N   GLU B  54 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU B  54 " occ=0.50
    residue:
      pdb=" N   GLU B 111 " occ=0.70
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 111 " occ=0.70
    residue:
      pdb=" N   MET C   1 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CE  MET C   1 " occ=0.50
    residue:
      pdb=" N   ARG C   5 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG C   5 " occ=0.50
    ... (remaining 15 not shown)
  Time building chain proxies: 1.74, per 1000 atoms: 0.29
  Number of scatterers: 6054
  At special positions: 0
  Unit cell: (114.126, 78.565, 81.046, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ni      2     28.00
     S      30     16.00
     P       1     15.00
     O    1185      8.00
     N    1048      7.00
     C    3788      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 382.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1416

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      35.0% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 26
      removed outlier: 3.515A  pdb=" N   LYS A   8 " --> pdb=" O   ASN A   4 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN A  12 " --> pdb=" O   LYS A   8 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A  13 " --> pdb=" O   GLU A   9 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ARG A  26 " --> pdb=" O   LYS A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 50
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 3.575A  pdb=" N   VAL A  69 " --> pdb=" O   ARG A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 77
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 3.736A  pdb=" N   VAL B  51 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 63
      removed outlier: 3.674A  pdb=" N   ILE B  63 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 120
    Processing helix  chain 'C' and resid 5 through 12
    Processing helix  chain 'C' and resid 144 through 151
      removed outlier: 3.737A  pdb=" N   VAL C 148 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 171
    Processing helix  chain 'C' and resid 176 through 187
    Processing helix  chain 'C' and resid 188 through 190
      No H-bonds generated for 'chain 'C' and resid 188 through 190'
    Processing helix  chain 'C' and resid 204 through 215
      removed outlier: 4.153A  pdb=" N   ILE C 208 " --> pdb=" O   SER C 204 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLN C 211 " --> pdb=" O   PRO C 207 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE C 212 " --> pdb=" O   ILE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 243
    Processing helix  chain 'C' and resid 258 through 267
    Processing helix  chain 'C' and resid 286 through 293
    Processing helix  chain 'C' and resid 308 through 318
      removed outlier: 4.400A  pdb=" N   ILE C 312 " --> pdb=" O   THR C 308 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ASP C 313 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU C 316 " --> pdb=" O   ILE C 312 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ASP C 317 " --> pdb=" O   ASP C 313 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   MET C 318 " --> pdb=" O   GLU C 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 322
    Processing helix  chain 'C' and resid 329 through 340
    Processing helix  chain 'C' and resid 341 through 354
      removed outlier: 3.583A  pdb=" N   ILE C 350 " --> pdb=" O   ALA C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 389
    Processing helix  chain 'C' and resid 399 through 408
    Processing helix  chain 'C' and resid 412 through 418
    Processing helix  chain 'C' and resid 480 through 484
      removed outlier: 6.769A  pdb=" N   GLY C 484 " --> pdb=" O   GLY C 481 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 485 through 490
      removed outlier: 3.764A  pdb=" N   ASP C 489 " --> pdb=" O   ASP C 485 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 496 through 503
    Processing helix  chain 'C' and resid 503 through 509
    Processing helix  chain 'C' and resid 524 through 528
    Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 86
    Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 13
    Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20
    Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 56
    Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 43
    Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 96
    Processing sheet with id=AA7, first strand: chain 'C' and resid 93 through 98
      removed outlier: 5.091A  pdb=" N   ILE C  94 " --> pdb=" O   LYS C  90 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LYS C  90 " --> pdb=" O   ILE C  94 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY C  96 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   TYR C  83 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   LEU C  75 " --> pdb=" O   TYR C  83 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   ALA C  85 " --> pdb=" O   ASN C  73 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  85 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   LEU C  70 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 93 through 98
      removed outlier: 5.091A  pdb=" N   ILE C  94 " --> pdb=" O   LYS C  90 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LYS C  90 " --> pdb=" O   ILE C  94 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY C  96 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   TYR C  83 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   LEU C  75 " --> pdb=" O   TYR C  83 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   ALA C  85 " --> pdb=" O   ASN C  73 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  85 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ALA C 131 " --> pdb=" O   LEU C  77 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   LYS C 452 " --> pdb=" O   ILE C 456 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   ILE C 456 " --> pdb=" O   LYS C 452 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 133 through 139
      removed outlier: 6.649A  pdb=" N   GLY C 133 " --> pdb=" O   THR C 156 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   PHE C 158 " --> pdb=" O   GLY C 133 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP C 135 " --> pdb=" O   PHE C 158 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   GLY C 160 " --> pdb=" O   ASP C 135 " (cutoff:3.500A)
      removed outlier: 9.065A  pdb=" N   HIS C 137 " --> pdb=" O   GLY C 160 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY C 218 " --> pdb=" O   ILE C 196 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   VAL C 246 " --> pdb=" O   HIS C 272 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE C 271 " --> pdb=" O   LEU C 297 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 139
      removed outlier: 6.649A  pdb=" N   GLY C 133 " --> pdb=" O   THR C 156 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   PHE C 158 " --> pdb=" O   GLY C 133 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP C 135 " --> pdb=" O   PHE C 158 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   GLY C 160 " --> pdb=" O   ASP C 135 " (cutoff:3.500A)
      removed outlier: 9.065A  pdb=" N   HIS C 137 " --> pdb=" O   GLY C 160 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ILE C 196 " --> pdb=" O   PHE C 494 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539

    234 hydrogen bonds defined for protein.
    627 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: 1.21

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2069
        1.34 -     1.46: 1058
        1.46 -     1.58: 2970
        1.58 -     1.69: 0
        1.69 -     1.81: 59
  Bond restraints: 6156
  Sorted by residual:
  bond pdb=" NZ  KCX C 220 "
       pdb=" CX  KCX C 220 "
    ideal  model  delta    sigma   weight residual
    1.411  1.331  0.080 2.00e-02 2.50e+03 1.61e+01
  bond pdb=" CE  KCX C 220 "
       pdb=" NZ  KCX C 220 "
    ideal  model  delta    sigma   weight residual
    1.442  1.492 -0.050 2.00e-02 2.50e+03 6.19e+00
  bond pdb=" SD  CXM A   1 "
       pdb=" CE  CXM A   1 "
    ideal  model  delta    sigma   weight residual
    1.808  1.763  0.045 2.00e-02 2.50e+03 4.99e+00
  bond pdb=" C   CXM A   1 "
       pdb=" O   CXM A   1 "
    ideal  model  delta    sigma   weight residual
    1.231  1.270 -0.039 2.00e-02 2.50e+03 3.78e+00
  bond pdb=" CA  CXM A   1 "
       pdb=" C   CXM A   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.563 -0.038 2.10e-02 2.27e+03 3.20e+00
  ... (remaining 6151 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 8223
        2.11 -     4.22: 87
        4.22 -     6.33: 17
        6.33 -     8.44: 6
        8.44 -    10.55: 1
  Bond angle restraints: 8334
  Sorted by residual:
  angle pdb=" CB  LYS C   2 "
        pdb=" CG  LYS C   2 "
        pdb=" CD  LYS C   2 "
      ideal   model   delta    sigma   weight residual
     111.30  121.85  -10.55 2.30e+00 1.89e-01 2.10e+01
  angle pdb=" N   ASP C 363 "
        pdb=" CA  ASP C 363 "
        pdb=" C   ASP C 363 "
      ideal   model   delta    sigma   weight residual
     111.28  106.16    5.12 1.35e+00 5.49e-01 1.44e+01
  angle pdb=" CA  GLN C 501 "
        pdb=" CB  GLN C 501 "
        pdb=" CG  GLN C 501 "
      ideal   model   delta    sigma   weight residual
     114.10  121.52   -7.42 2.00e+00 2.50e-01 1.38e+01
  angle pdb=" CA  GLN B 115 "
        pdb=" CB  GLN B 115 "
        pdb=" CG  GLN B 115 "
      ideal   model   delta    sigma   weight residual
     114.10  121.40   -7.30 2.00e+00 2.50e-01 1.33e+01
  angle pdb=" CB  GLN B 115 "
        pdb=" CG  GLN B 115 "
        pdb=" CD  GLN B 115 "
      ideal   model   delta    sigma   weight residual
     112.60  118.45   -5.85 1.70e+00 3.46e-01 1.18e+01
  ... (remaining 8329 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 3122
       17.37 -    34.74: 426
       34.74 -    52.11: 120
       52.11 -    69.49: 32
       69.49 -    86.86: 12
  Dihedral angle restraints: 3712
    sinusoidal: 1489
      harmonic: 2223
  Sorted by residual:
  dihedral pdb=" CA  ASP C 363 "
           pdb=" C   ASP C 363 "
           pdb=" N   ALA C 364 "
           pdb=" CA  ALA C 364 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.40  -24.60     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" CA  TRP C 438 "
           pdb=" C   TRP C 438 "
           pdb=" N   GLU C 439 "
           pdb=" CA  GLU C 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.83   18.17     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  MET C 563 "
           pdb=" C   MET C 563 "
           pdb=" N   ALA C 564 "
           pdb=" CA  ALA C 564 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.35  -17.65     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 3709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 574
       0.032 -    0.064: 216
       0.064 -    0.096: 92
       0.096 -    0.128: 53
       0.128 -    0.160: 6
  Chirality restraints: 941
  Sorted by residual:
  chirality pdb=" CG  LEU B 114 "
            pdb=" CB  LEU B 114 "
            pdb=" CD1 LEU B 114 "
            pdb=" CD2 LEU B 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  ASN C 302 "
            pdb=" N   ASN C 302 "
            pdb=" C   ASN C 302 "
            pdb=" CB  ASN C 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  ILE C  97 "
            pdb=" N   ILE C  97 "
            pdb=" C   ILE C  97 "
            pdb=" CB  ILE C  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.65e-01
  ... (remaining 938 not shown)

  Planarity restraints: 1100
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 284 "    0.035 5.00e-02 4.00e+02   5.20e-02 4.32e+00
        pdb=" N   PRO C 285 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C 285 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 285 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A  34 "    0.007 2.00e-02 2.50e+03   1.46e-02 2.14e+00
        pdb=" CD  GLU A  34 "   -0.025 2.00e-02 2.50e+03
        pdb=" OE1 GLU A  34 "    0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU A  34 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  32 "   -0.022 5.00e-02 4.00e+02   3.36e-02 1.80e+00
        pdb=" N   PRO A  33 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A  33 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  33 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1097 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 77
        2.54 -     3.13: 4633
        3.13 -     3.72: 9742
        3.72 -     4.31: 14240
        4.31 -     4.90: 23690
  Nonbonded interactions: 52382
  Sorted by model distance:
  nonbonded pdb=" OQ1 KCX C 220 "
            pdb="NI    NI C 601 "
     model   vdw
     1.955 2.180
  nonbonded pdb=" NE2 HIS C 275 "
            pdb="NI    NI C 601 "
     model   vdw
     1.956 2.260
  nonbonded pdb=" NE2 HIS C 139 "
            pdb="NI    NI C 602 "
     model   vdw
     1.959 2.260
  nonbonded pdb=" OQ2 KCX C 220 "
            pdb="NI    NI C 602 "
     model   vdw
     1.988 2.180
  nonbonded pdb="NI    NI C 601 "
            pdb=" O1  2PA C 603 "
     model   vdw
     2.005 2.180
  ... (remaining 52377 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.50 max=1.00 mean=0.98
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:             1.340
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.030
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:7.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
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      :  0.003   0.080   6156  Z= 0.143
  Angle     :  0.586  10.551   8334  Z= 0.300
  Chirality :  0.045   0.160    941
  Planarity :  0.004   0.052   1100
  Dihedral  : 18.053  86.858   2296
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.58 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 28.04 %
    Favored  : 66.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.42 (0.30), residues: 782
  helix:  1.19 (0.37), residues: 208
  sheet:  0.50 (0.48), residues: 105
  loop : -0.13 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 449 
 TYR   0.017   0.001   TYR A  32 
 PHE   0.004   0.001   PHE C 442 
 TRP   0.016   0.001   TRP C 438 
 HIS   0.007   0.001   HIS C 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6156)
  covalent geometry    : angle       0.58642 ( 8334)
  hydrogen bonds       : bond        0.16325 (  222)
  hydrogen bonds       : angle       6.83061 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: B   76 ARG cc_start: 0.9128 (ttm-80) cc_final: 0.8853 (ttm-80)
REVERT: C  320 MET cc_start: 0.5546 (mmt) cc_final: 0.5084 (tmt)
  outliers start: 32
  outliers final: 27
  residues processed: 123
  average time/residue: 0.5586
  time to fit residues: 72.0557
Evaluate side-chains
  113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   33 SER
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue   71 LEU
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  147 ASP
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  186 SER
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  299 SER
Chi-restraints excluded: chain C residue  314 GLU
Chi-restraints excluded: chain C residue  467 SER
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  516 THR
Chi-restraints excluded: chain C residue  551 GLU
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
B  22 ASN
B  68 ASN
B 104 ASN
C 142 ASN
C 245 GLN
C 293 HIS
C 315 HIS
C 387 GLN
C 418 GLN
** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 522 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.113597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.092462 restraints weight = 8987.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 1.83
r_work: 0.3000 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6156  Z= 0.169
  Angle     :  0.568   7.759   8334  Z= 0.294
  Chirality :  0.047   0.188    941
  Planarity :  0.004   0.052   1100
  Dihedral  :  7.223  52.012    891
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.96 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 24.92 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.49 (0.31), residues: 782
  helix:  1.08 (0.35), residues: 230
  sheet:  0.81 (0.48), residues: 97
  loop : -0.12 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 566 
 TYR   0.014   0.001   TYR B   6 
 PHE   0.007   0.001   PHE B  48 
 TRP   0.013   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6156)
  covalent geometry    : angle       0.56831 ( 8334)
  hydrogen bonds       : bond        0.04049 (  222)
  hydrogen bonds       : angle       4.90102 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 0.252 
Fit side-chains
REVERT: B   31 ARG cc_start: 0.8320 (mtp-110) cc_final: 0.7941 (ttm110)
REVERT: B   82 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7927 (pp20)
REVERT: C  320 MET cc_start: 0.5766 (mmt) cc_final: 0.5140 (tmt)
REVERT: C  547 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8480 (ttpp)
  outliers start: 32
  outliers final: 9
  residues processed: 115
  average time/residue: 0.6292
  time to fit residues: 75.4925
Evaluate side-chains
  93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  551 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 47 optimal weight:    9.9990
   chunk 52 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.110658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.089623 restraints weight = 8826.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 1.78
r_work: 0.2952 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6156  Z= 0.130
  Angle     :  0.536   7.569   8334  Z= 0.273
  Chirality :  0.046   0.209    941
  Planarity :  0.004   0.053   1100
  Dihedral  :  5.548  47.774    863
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.58 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 24.77 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.49 (0.31), residues: 782
  helix:  1.05 (0.35), residues: 232
  sheet:  0.80 (0.47), residues: 97
  loop : -0.09 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 566 
 TYR   0.008   0.001   TYR B   6 
 PHE   0.005   0.001   PHE B  48 
 TRP   0.014   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6156)
  covalent geometry    : angle       0.53557 ( 8334)
  hydrogen bonds       : bond        0.03606 (  222)
  hydrogen bonds       : angle       4.65804 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.252 
Fit side-chains
REVERT: B   82 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7791 (tm-30)
REVERT: C  320 MET cc_start: 0.5591 (mmt) cc_final: 0.5011 (tmt)
REVERT: C  470 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8113 (p)
  outliers start: 29
  outliers final: 12
  residues processed: 108
  average time/residue: 0.6105
  time to fit residues: 69.0948
Evaluate side-chains
  99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  315 HIS
Chi-restraints excluded: chain C residue  360 MET
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  498 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 10 optimal weight:    0.4980
   chunk 68 optimal weight:    0.0060
   chunk 41 optimal weight:    0.9980
   chunk 61 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.6596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.112174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.091447 restraints weight = 8935.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.76
r_work: 0.2995 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6156  Z= 0.103
  Angle     :  0.522   7.559   8334  Z= 0.267
  Chirality :  0.045   0.212    941
  Planarity :  0.004   0.054   1100
  Dihedral  :  4.961  42.333    859
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.07 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 25.39 %
    Favored  : 70.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.59 (0.31), residues: 782
  helix:  1.16 (0.35), residues: 232
  sheet:  0.87 (0.48), residues: 97
  loop : -0.05 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  94 
 TYR   0.007   0.001   TYR C  79 
 PHE   0.004   0.001   PHE C 442 
 TRP   0.014   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6156)
  covalent geometry    : angle       0.52204 ( 8334)
  hydrogen bonds       : bond        0.03163 (  222)
  hydrogen bonds       : angle       4.45932 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.243 
Fit side-chains
REVERT: B   28 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8758 (p)
REVERT: B   31 ARG cc_start: 0.8364 (mtp-110) cc_final: 0.7458 (mtp-110)
REVERT: C  320 MET cc_start: 0.5597 (mmt) cc_final: 0.5012 (tmt)
REVERT: C  386 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7928 (mttt)
  outliers start: 24
  outliers final: 8
  residues processed: 104
  average time/residue: 0.5697
  time to fit residues: 62.0711
Evaluate side-chains
  90 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  315 HIS
Chi-restraints excluded: chain C residue  386 LYS
Chi-restraints excluded: chain C residue  498 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    1.2786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.110517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.089648 restraints weight = 9011.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 1.79
r_work: 0.2978 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6156  Z= 0.124
  Angle     :  0.540   8.009   8334  Z= 0.273
  Chirality :  0.045   0.234    941
  Planarity :  0.004   0.060   1100
  Dihedral  :  4.752  36.810    858
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.58 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 26.01 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.59 (0.31), residues: 782
  helix:  1.16 (0.35), residues: 232
  sheet:  0.78 (0.48), residues: 96
  loop : -0.03 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  94 
 TYR   0.006   0.001   TYR C  79 
 PHE   0.005   0.001   PHE B  48 
 TRP   0.012   0.001   TRP C 438 
 HIS   0.004   0.001   HIS C 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6156)
  covalent geometry    : angle       0.54015 ( 8334)
  hydrogen bonds       : bond        0.03260 (  222)
  hydrogen bonds       : angle       4.45374 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.323 
Fit side-chains
REVERT: B   28 THR cc_start: 0.9089 (m) cc_final: 0.8801 (p)
REVERT: B   31 ARG cc_start: 0.8393 (mtp-110) cc_final: 0.8108 (mtp180)
REVERT: B   81 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6976 (pp20)
REVERT: B   83 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6414 (mmm)
REVERT: C  320 MET cc_start: 0.5576 (mmt) cc_final: 0.5351 (mmm)
REVERT: C  367 MET cc_start: 0.8482 (mtp) cc_final: 0.8042 (mtt)
  outliers start: 21
  outliers final: 13
  residues processed: 99
  average time/residue: 0.5608
  time to fit residues: 58.4025
Evaluate side-chains
  94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   81 GLU
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  315 HIS
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  489 ASP
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0970
   chunk 69 optimal weight:    0.1980
   chunk 67 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.2382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.110649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.089810 restraints weight = 8952.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 1.78
r_work: 0.2979 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6156  Z= 0.122
  Angle     :  0.526   7.324   8334  Z= 0.269
  Chirality :  0.045   0.220    941
  Planarity :  0.004   0.054   1100
  Dihedral  :  4.569  29.507    857
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.58 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 25.70 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.57 (0.31), residues: 782
  helix:  1.15 (0.35), residues: 231
  sheet:  0.74 (0.47), residues: 96
  loop : -0.03 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 305 
 TYR   0.006   0.001   TYR C  79 
 PHE   0.005   0.001   PHE B  48 
 TRP   0.012   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6156)
  covalent geometry    : angle       0.52579 ( 8334)
  hydrogen bonds       : bond        0.03218 (  222)
  hydrogen bonds       : angle       4.42054 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.247 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8407 (mt)
REVERT: B   28 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8826 (p)
REVERT: B   31 ARG cc_start: 0.8348 (mtp-110) cc_final: 0.7991 (mtp180)
REVERT: C    2 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8555 (mmmt)
REVERT: C  320 MET cc_start: 0.5598 (mmt) cc_final: 0.5393 (mmm)
REVERT: C  385 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8291 (tttt)
REVERT: C  386 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7945 (mttt)
REVERT: C  470 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8144 (p)
  outliers start: 23
  outliers final: 11
  residues processed: 102
  average time/residue: 0.5366
  time to fit residues: 57.4696
Evaluate side-chains
  98 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  315 HIS
Chi-restraints excluded: chain C residue  385 LYS
Chi-restraints excluded: chain C residue  386 LYS
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 26 optimal weight:    0.1980
   chunk 22 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.4384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.110144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.089331 restraints weight = 9014.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 1.78
r_work: 0.2966 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6156  Z= 0.132
  Angle     :  0.551   8.452   8334  Z= 0.278
  Chirality :  0.046   0.237    941
  Planarity :  0.004   0.052   1100
  Dihedral  :  4.510  27.899    857
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.71 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 26.48 %
    Favored  : 70.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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 (0.31), residues: 782
  helix:  1.10 (0.35), residues: 231
  sheet:  0.72 (0.47), residues: 96
  loop : -0.03 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  94 
 TYR   0.006   0.001   TYR B   6 
 PHE   0.006   0.001   PHE B  48 
 TRP   0.011   0.001   TRP C 438 
 HIS   0.004   0.001   HIS C 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6156)
  covalent geometry    : angle       0.55080 ( 8334)
  hydrogen bonds       : bond        0.03278 (  222)
  hydrogen bonds       : angle       4.42796 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.260 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8454 (mt)
REVERT: B   28 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8818 (p)
REVERT: C    2 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8538 (mmmt)
REVERT: C  320 MET cc_start: 0.5576 (mmt) cc_final: 0.5357 (mmm)
REVERT: C  367 MET cc_start: 0.8516 (mtp) cc_final: 0.8040 (mtt)
REVERT: C  385 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8277 (tttt)
REVERT: C  386 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7954 (mttt)
  outliers start: 19
  outliers final: 11
  residues processed: 96
  average time/residue: 0.5759
  time to fit residues: 58.0276
Evaluate side-chains
  96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  315 HIS
Chi-restraints excluded: chain C residue  385 LYS
Chi-restraints excluded: chain C residue  386 LYS
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 47 optimal weight:    9.9990
   chunk 57 optimal weight:    8.9990
   chunk 73 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0670
   chunk 40 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 12 optimal weight:    9.9990
   chunk 68 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.8320

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.111462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.090756 restraints weight = 8981.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 1.78
r_work: 0.2988 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2889
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2889
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6156  Z= 0.108
  Angle     :  0.534   7.079   8334  Z= 0.274
  Chirality :  0.045   0.230    941
  Planarity :  0.004   0.053   1100
  Dihedral  :  4.372  26.254    856
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.20 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 27.10 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.63 (0.31), residues: 782
  helix:  1.16 (0.35), residues: 235
  sheet:  0.76 (0.48), residues: 96
  loop :  0.03 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 116 
 TYR   0.006   0.001   TYR C  79 
 PHE   0.004   0.000   PHE B  48 
 TRP   0.013   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6156)
  covalent geometry    : angle       0.53401 ( 8334)
  hydrogen bonds       : bond        0.03071 (  222)
  hydrogen bonds       : angle       4.36252 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.228 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8436 (mt)
REVERT: B   28 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8859 (p)
REVERT: B   31 ARG cc_start: 0.8565 (mtp180) cc_final: 0.8146 (mmm160)
REVERT: C    2 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8527 (mmmt)
REVERT: C  320 MET cc_start: 0.5583 (mmt) cc_final: 0.5369 (mmm)
REVERT: C  385 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8247 (tttt)
REVERT: C  386 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7946 (mttt)
REVERT: C  470 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8019 (p)
  outliers start: 18
  outliers final: 8
  residues processed: 102
  average time/residue: 0.5558
  time to fit residues: 59.5980
Evaluate side-chains
  97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  315 HIS
Chi-restraints excluded: chain C residue  385 LYS
Chi-restraints excluded: chain C residue  386 LYS
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 52 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 74 optimal weight:    0.1980
   chunk 25 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0470
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.4878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.113552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.093276 restraints weight = 8974.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 1.77
r_work: 0.3019 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6156  Z= 0.101
  Angle     :  0.551   9.390   8334  Z= 0.277
  Chirality :  0.046   0.304    941
  Planarity :  0.004   0.065   1100
  Dihedral  :  4.240  24.449    856
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.58 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 28.19 %
    Favored  : 69.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.71 (0.31), residues: 782
  helix:  1.20 (0.35), residues: 236
  sheet:  0.86 (0.51), residues: 87
  loop :  0.09 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 116 
 TYR   0.007   0.001   TYR C  79 
 PHE   0.003   0.000   PHE C 442 
 TRP   0.014   0.001   TRP C 438 
 HIS   0.003   0.001   HIS C 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 6156)
  covalent geometry    : angle       0.55119 ( 8334)
  hydrogen bonds       : bond        0.02873 (  222)
  hydrogen bonds       : angle       4.27693 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: B    7 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8420 (mt)
REVERT: B   28 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8884 (p)
REVERT: B  112 LEU cc_start: 0.8708 (tm) cc_final: 0.8484 (tm)
REVERT: C    2 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8446 (mmmt)
REVERT: C  255 GLU cc_start: 0.8367 (tt0) cc_final: 0.7755 (tp30)
REVERT: C  320 MET cc_start: 0.5624 (mmt) cc_final: 0.5371 (mmm)
REVERT: C  367 MET cc_start: 0.8437 (mtp) cc_final: 0.8013 (mtt)
REVERT: C  385 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8272 (tttt)
REVERT: C  470 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8125 (p)
  outliers start: 14
  outliers final: 6
  residues processed: 102
  average time/residue: 0.5876
  time to fit residues: 62.8173
Evaluate side-chains
  94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  315 HIS
Chi-restraints excluded: chain C residue  385 LYS
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 18 optimal weight:   20.0000
   chunk 48 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    1.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.114038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.093493 restraints weight = 8967.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.76
r_work: 0.3051 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2943
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2943
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6156  Z= 0.140
  Angle     :  0.577   8.459   8334  Z= 0.294
  Chirality :  0.046   0.254    941
  Planarity :  0.005   0.070   1100
  Dihedral  :  4.359  26.247    856
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.45 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 28.97 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.69 (0.31), residues: 782
  helix:  1.15 (0.35), residues: 235
  sheet:  1.02 (0.47), residues: 95
  loop :  0.04 (0.32), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 116 
 TYR   0.007   0.001   TYR B   6 
 PHE   0.007   0.001   PHE B  48 
 TRP   0.011   0.001   TRP C 438 
 HIS   0.007   0.001   HIS C 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6156)
  covalent geometry    : angle       0.57659 ( 8334)
  hydrogen bonds       : bond        0.03260 (  222)
  hydrogen bonds       : angle       4.39761 (  627)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B    7 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8545 (mt)
REVERT: C    2 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8518 (mmmt)
REVERT: C  255 GLU cc_start: 0.8443 (tt0) cc_final: 0.7884 (tp30)
  outliers start: 10
  outliers final: 7
  residues processed: 93
  average time/residue: 0.5860
  time to fit residues: 57.1722
Evaluate side-chains
  93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain C residue  315 HIS
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  552 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
C 315 HIS
C 324 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.113777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.093431 restraints weight = 8961.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.75
r_work: 0.3052 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6156  Z= 0.133
  Angle     :  0.591   9.840   8334  Z= 0.299
  Chirality :  0.047   0.311    941
  Planarity :  0.005   0.068   1100
  Dihedral  :  4.358  26.589    856
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.32 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 28.82 %
    Favored  : 69.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.61 (0.31), residues: 782
  helix:  1.09 (0.35), residues: 231
  sheet:  1.00 (0.47), residues: 95
  loop : -0.01 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 116 
 TYR   0.006   0.001   TYR B   6 
 PHE   0.005   0.001   PHE B  48 
 TRP   0.012   0.001   TRP C 438 
 HIS   0.011   0.001   HIS C 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6156)
  covalent geometry    : angle       0.59094 ( 8334)
  hydrogen bonds       : bond        0.03290 (  222)
  hydrogen bonds       : angle       4.36889 (  627)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2384.37 seconds
wall clock time: 41 minutes 25.26 seconds (2485.26 seconds total)