Starting phenix.real_space_refine
on Tue Mar 11 18:22:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8scx_40346/03_2025/8scx_40346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8scx_40346/03_2025/8scx_40346.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8scx_40346/03_2025/8scx_40346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8scx_40346/03_2025/8scx_40346.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8scx_40346/03_2025/8scx_40346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8scx_40346/03_2025/8scx_40346.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      29      5.16       5
     C    3659      2.51       5
     N     992      2.21       5
     O    1070      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5753
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 978
          Classifications: {'peptide': 133}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 127}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 971
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 128}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1947
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 256}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 179
          Unresolved non-hydrogen angles: 216
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 82
    Chain: "L"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 837
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "H"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 901
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 69
          Unusual residues: {'CDL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 31
    Chain: "B"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 50
          Unusual residues: {'PTY': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.27, per 1000 atoms: 0.74
  Number of scatterers: 5753
  At special positions: 0
  Unit cell: (94.5, 75.6, 116.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     P       3     15.00
     O    1070      8.00
     N     992      7.00
     C    3659      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  10 " - pdb=" SG  CYS A  77 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 114 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.77
  Conformation dependent library (CDL) restraints added in 790.5 milliseconds
  

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1352

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 8 sheets defined
      53.6% alpha, 25.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 41
      removed outlier: 3.708A  pdb=" N   ILE A  14 " --> pdb=" O   CYS A  10 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   LEU A  15 " --> pdb=" O   PRO A  11 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ASN A  16 " --> pdb=" O   ILE A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 45 through 84
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 89 through 103
    Processing helix  chain 'A' and resid 104 through 106
      No H-bonds generated for 'chain 'A' and resid 104 through 106'
    Processing helix  chain 'A' and resid 107 through 138
    Processing helix  chain 'B' and resid 92 through 122
      removed outlier: 3.755A  pdb=" N   ASP B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 171
      Proline residue:  B 146  - end of helix
    Processing helix  chain 'B' and resid 174 through 190
    Processing helix  chain 'B' and resid 195 through 220
      removed outlier: 3.936A  pdb=" N   GLY B 199 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR B 200 " --> pdb=" O   LYS B 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 126
    Processing helix  chain 'C' and resid 126 through 152
      Proline residue:  C 149  - end of helix
    Processing helix  chain 'C' and resid 153 through 164
      removed outlier: 3.586A  pdb=" N   LYS C 157 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 172
      removed outlier: 3.730A  pdb=" N   SER C 169 " --> pdb=" O   GLY C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 190
    Processing helix  chain 'C' and resid 256 through 266
      removed outlier: 3.554A  pdb=" N   PHE C 265 " --> pdb=" O   VAL C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 281
    Processing helix  chain 'C' and resid 285 through 296
    Processing helix  chain 'C' and resid 296 through 307
    Processing helix  chain 'C' and resid 309 through 317
      removed outlier: 3.758A  pdb=" N   LYS C 315 " --> pdb=" O   LYS C 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 335
      removed outlier: 3.614A  pdb=" N   GLU C 334 " --> pdb=" O   LYS C 330 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 105 through 109
      removed outlier: 3.504A  pdb=" N   THR H 109 " --> pdb=" O   ALA H 106 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 119 through 121
      No H-bonds generated for 'chain 'H' and resid 119 through 121'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 337 through 339
      removed outlier: 6.246A  pdb=" N   ILE C 362 " --> pdb=" O   LYS C 355 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LYS C 355 " --> pdb=" O   ILE C 362 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   VAL C 364 " --> pdb=" O   SER C 353 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   SER C 353 " --> pdb=" O   VAL C 364 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   VAL C 366 " --> pdb=" O   ILE C 351 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   ILE C 351 " --> pdb=" O   VAL C 366 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLY C 368 " --> pdb=" O   VAL C 349 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   VAL C 349 " --> pdb=" O   GLY C 368 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP C 345 " --> pdb=" O   GLN C 372 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ILE C 374 " --> pdb=" O   ILE C 343 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   ILE C 343 " --> pdb=" O   ILE C 374 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 337 through 339
      removed outlier: 5.110A  pdb=" N   ARG C 404 " --> pdb=" O   PRO C 363 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ASN C 375 " --> pdb=" O   ASN C 392 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ASN C 392 " --> pdb=" O   ASN C 375 " (cutoff:3.500A)
      removed outlier: 9.467A  pdb=" N   TYR C 377 " --> pdb=" O   GLU C 390 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   GLU C 390 " --> pdb=" O   TYR C 377 " (cutoff:3.500A)
      removed outlier: 10.715A  pdb=" N   LYS C 379 " --> pdb=" O   GLY C 388 " (cutoff:3.500A)
      removed outlier: 12.824A  pdb=" N   GLY C 388 " --> pdb=" O   LYS C 379 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU C 421 " --> pdb=" O   VAL C 401 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   THR C 403 " --> pdb=" O   ILE C 419 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   ILE C 419 " --> pdb=" O   THR C 403 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 24 through 27
      removed outlier: 3.595A  pdb=" N   ASP L  94 " --> pdb=" O   SER L  91 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER L  96 " --> pdb=" O   SER L  89 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 30 through 33
      removed outlier: 6.922A  pdb=" N   LEU L  31 " --> pdb=" O   GLU L 129 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   MET L  57 " --> pdb=" O   TYR L  73 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   TYR L  73 " --> pdb=" O   MET L  57 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   TRP L  59 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 50 through 51
    Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 26
    Processing sheet with id=AA7, first strand: chain 'H' and resid 76 through 78
      removed outlier: 6.814A  pdb=" N   TRP H  55 " --> pdb=" O   LEU H  67 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   VAL H  69 " --> pdb=" O   VAL H  53 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL H  53 " --> pdb=" O   VAL H  69 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   GLY H  52 " --> pdb=" O   TYR H 117 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE H 111 " --> pdb=" O   GLN H  58 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TYR H 125 " --> pdb=" O   ARG H 116 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 76 through 78
      removed outlier: 6.814A  pdb=" N   TRP H  55 " --> pdb=" O   LEU H  67 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   VAL H  69 " --> pdb=" O   VAL H  53 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL H  53 " --> pdb=" O   VAL H  69 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   GLY H  52 " --> pdb=" O   TYR H 117 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE H 111 " --> pdb=" O   GLN H  58 " (cutoff:3.500A)

    399 hydrogen bonds defined for protein.
    1146 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: 1.65

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1864
        1.34 -     1.47: 1441
        1.47 -     1.60: 2510
        1.60 -     1.72: 6
        1.72 -     1.85: 46
  Bond restraints: 5867
  Sorted by residual:
  bond pdb=" CA7 CDL A 301 "
       pdb=" OA8 CDL A 301 "
    ideal  model  delta    sigma   weight residual
    1.334  1.451 -0.117 1.10e-02 8.26e+03 1.12e+02
  bond pdb=" CB7 CDL A 301 "
       pdb=" OB8 CDL A 301 "
    ideal  model  delta    sigma   weight residual
    1.334  1.448 -0.114 1.10e-02 8.26e+03 1.07e+02
  bond pdb=" CA5 CDL A 301 "
       pdb=" OA6 CDL A 301 "
    ideal  model  delta    sigma   weight residual
    1.342  1.450 -0.108 1.50e-02 4.44e+03 5.23e+01
  bond pdb=" CB5 CDL A 301 "
       pdb=" OB6 CDL A 301 "
    ideal  model  delta    sigma   weight residual
    1.342  1.447 -0.105 1.50e-02 4.44e+03 4.94e+01
  bond pdb=" C8  PTY B 301 "
       pdb=" O7  PTY B 301 "
    ideal  model  delta    sigma   weight residual
    1.331  1.453 -0.122 2.00e-02 2.50e+03 3.70e+01
  ... (remaining 5862 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 7731
        1.97 -     3.93: 139
        3.93 -     5.90: 33
        5.90 -     7.86: 3
        7.86 -     9.83: 8
  Bond angle restraints: 7914
  Sorted by residual:
  angle pdb=" C11 CDL A 301 "
        pdb=" CA5 CDL A 301 "
        pdb=" OA6 CDL A 301 "
      ideal   model   delta    sigma   weight residual
     111.33  120.47   -9.14 1.32e+00 5.72e-01 4.78e+01
  angle pdb=" C51 CDL A 301 "
        pdb=" CB5 CDL A 301 "
        pdb=" OB6 CDL A 301 "
      ideal   model   delta    sigma   weight residual
     111.33  120.29   -8.96 1.32e+00 5.72e-01 4.59e+01
  angle pdb=" C31 CDL A 301 "
        pdb=" CA7 CDL A 301 "
        pdb=" OA8 CDL A 301 "
      ideal   model   delta    sigma   weight residual
     111.64  121.24   -9.60 1.65e+00 3.69e-01 3.40e+01
  angle pdb=" C71 CDL A 301 "
        pdb=" CB7 CDL A 301 "
        pdb=" OB8 CDL A 301 "
      ideal   model   delta    sigma   weight residual
     111.64  120.69   -9.05 1.65e+00 3.69e-01 3.02e+01
  angle pdb=" OB6 CDL A 301 "
        pdb=" CB5 CDL A 301 "
        pdb=" OB7 CDL A 301 "
      ideal   model   delta    sigma   weight residual
     123.92  118.79    5.13 1.00e+00 9.92e-01 2.61e+01
  ... (remaining 7909 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.64: 3281
       24.64 -    49.29: 173
       49.29 -    73.93: 26
       73.93 -    98.57: 6
       98.57 -   123.22: 1
  Dihedral angle restraints: 3487
    sinusoidal: 1359
      harmonic: 2128
  Sorted by residual:
  dihedral pdb=" CB  CYS A  10 "
           pdb=" SG  CYS A  10 "
           pdb=" SG  CYS A  77 "
           pdb=" CB  CYS A  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.91   35.91     1      1.00e+01 1.00e-02 1.82e+01
  dihedral pdb=" N1  PTY B 301 "
           pdb=" C2  PTY B 301 "
           pdb=" C3  PTY B 301 "
           pdb=" O11 PTY B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.33  -57.89  123.22     1      3.00e+01 1.11e-03 1.65e+01
  dihedral pdb=" CA  ASP A  17 "
           pdb=" C   ASP A  17 "
           pdb=" N   PHE A  18 "
           pdb=" CA  PHE A  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.46   18.54     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 3484 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 569
       0.033 -    0.066: 195
       0.066 -    0.099: 59
       0.099 -    0.132: 31
       0.132 -    0.166: 2
  Chirality restraints: 856
  Sorted by residual:
  chirality pdb=" CB  THR L 107 "
            pdb=" CA  THR L 107 "
            pdb=" OG1 THR L 107 "
            pdb=" CG2 THR L 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.17 2.00e-01 2.50e+01 6.86e-01
  chirality pdb=" CA  ILE L 130 "
            pdb=" N   ILE L 130 "
            pdb=" C   ILE L 130 "
            pdb=" CB  ILE L 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.56e-01
  chirality pdb=" CA  ILE L  72 "
            pdb=" N   ILE L  72 "
            pdb=" C   ILE L  72 "
            pdb=" CB  ILE L  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.23e-01
  ... (remaining 853 not shown)

  Planarity restraints: 1015
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  87 "    0.026 5.00e-02 4.00e+02   3.97e-02 2.52e+00
        pdb=" N   PRO A  88 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A  88 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  88 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN C 179 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.57e+00
        pdb=" CD  GLN C 179 "    0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLN C 179 "   -0.008 2.00e-02 2.50e+03
        pdb=" NE2 GLN C 179 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 145 "    0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO B 146 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 146 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 146 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1012 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1171
        2.77 -     3.30: 5340
        3.30 -     3.84: 9508
        3.84 -     4.37: 11499
        4.37 -     4.90: 20429
  Nonbonded interactions: 47947
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP L  50 "
            pdb=" OG  SER L  55 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD1 ASP C 361 "
            pdb=" NH1 ARG H  72 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" NZ  LYS L  63 "
            pdb=" O   ASP L 105 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   ASN C 286 "
            pdb=" OG1 THR C 290 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" NH2 ARG A  83 "
            pdb=" OD2 ASP A  87 "
     model   vdw
     2.301 3.120
  ... (remaining 47942 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.040
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
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      :  0.006   0.122   5867  Z= 0.380
  Angle     :  0.704   9.828   7914  Z= 0.378
  Chirality :  0.041   0.166    856
  Planarity :  0.003   0.040   1015
  Dihedral  : 14.972 123.216   2126
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.18 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.31), residues: 748
  helix:  1.78 (0.27), residues: 360
  sheet:  0.10 (0.44), residues: 144
  loop :  0.01 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  66 
 HIS   0.004   0.001   HIS A  33 
 PHE   0.008   0.001   PHE L  95 
 TYR   0.013   0.001   TYR H 117 
 ARG   0.002   0.000   ARG H 116 

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.668 
Fit side-chains
REVERT: C  157 LYS cc_start: 0.8722 (mptt) cc_final: 0.8488 (mptp)
  outliers start: 1
  outliers final: 0
  residues processed: 120
  average time/residue: 1.1940
  time to fit residues: 149.8259
Evaluate side-chains
  91 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    8.9990
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 35 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 163 ASN
B 173 HIS
C 392 ASN
L  62 GLN
H  58 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.109995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.079538 restraints weight = 8955.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.14
r_work: 0.2848 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5867  Z= 0.288
  Angle     :  0.549   5.496   7914  Z= 0.292
  Chirality :  0.043   0.135    856
  Planarity :  0.004   0.044   1015
  Dihedral  : 10.291  78.911    919
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 10.59 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.31), residues: 748
  helix:  2.47 (0.25), residues: 375
  sheet:  0.13 (0.44), residues: 144
  loop : -0.06 (0.43), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  66 
 HIS   0.004   0.001   HIS H  54 
 PHE   0.015   0.001   PHE A  18 
 TYR   0.014   0.001   TYR H 117 
 ARG   0.004   0.000   ARG L  44 

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A  131 MET cc_start: 0.8083 (tmm) cc_final: 0.7003 (mmp)
REVERT: C  157 LYS cc_start: 0.8519 (mptt) cc_final: 0.8198 (mptp)
REVERT: C  413 GLU cc_start: 0.8618 (tp30) cc_final: 0.8413 (tp30)
REVERT: H   35 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8220 (mp10)
REVERT: H  105 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7981 (mm-40)
  outliers start: 13
  outliers final: 4
  residues processed: 106
  average time/residue: 1.1215
  time to fit residues: 124.6822
Evaluate side-chains
  100 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain C residue  429 GLN
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain H residue   35 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 0 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
C 392 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.107356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.076652 restraints weight = 9051.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 2.13
r_work: 0.2790 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.056   5867  Z= 0.501
  Angle     :  0.604   5.829   7914  Z= 0.319
  Chirality :  0.046   0.143    856
  Planarity :  0.004   0.041   1015
  Dihedral  : 10.793  71.986    919
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 13.11 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.31), residues: 748
  helix:  2.60 (0.26), residues: 369
  sheet: -0.01 (0.44), residues: 142
  loop : -0.27 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H  66 
 HIS   0.004   0.001   HIS H  54 
 PHE   0.014   0.002   PHE C 322 
 TYR   0.016   0.002   TYR H 117 
 ARG   0.003   0.001   ARG L  44 

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8341 (tt0) cc_final: 0.7560 (tm-30)
REVERT: A  109 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7072 (mtm-85)
REVERT: A  131 MET cc_start: 0.8016 (tmm) cc_final: 0.7017 (mmp)
REVERT: B  144 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7557 (tpm-80)
REVERT: C  157 LYS cc_start: 0.8518 (mptt) cc_final: 0.8212 (mptp)
REVERT: C  413 GLU cc_start: 0.8565 (tp30) cc_final: 0.8338 (tp30)
REVERT: H   35 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8233 (mp10)
REVERT: H   91 ASP cc_start: 0.8093 (t70) cc_final: 0.7706 (t70)
REVERT: H  105 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8071 (mm-40)
  outliers start: 19
  outliers final: 6
  residues processed: 103
  average time/residue: 1.3685
  time to fit residues: 146.9042
Evaluate side-chains
  99 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain C residue  382 THR
Chi-restraints excluded: chain C residue  429 GLN
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain H residue   35 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 392 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.110102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.079544 restraints weight = 9034.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.15
r_work: 0.2843 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5867  Z= 0.225
  Angle     :  0.499   5.198   7914  Z= 0.266
  Chirality :  0.041   0.139    856
  Planarity :  0.004   0.042   1015
  Dihedral  :  9.944  69.705    919
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.54 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.31), residues: 748
  helix:  2.80 (0.26), residues: 377
  sheet:  0.04 (0.43), residues: 144
  loop : -0.14 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  54 
 PHE   0.011   0.001   PHE C 322 
 TYR   0.013   0.001   TYR H 117 
 ARG   0.002   0.000   ARG L  44 

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8256 (tt0) cc_final: 0.7568 (tm-30)
REVERT: A  109 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7048 (mtm-85)
REVERT: A  131 MET cc_start: 0.7998 (tmm) cc_final: 0.7073 (mmp)
REVERT: B  144 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7580 (tpm-80)
REVERT: C  157 LYS cc_start: 0.8550 (mptt) cc_final: 0.8209 (mptp)
REVERT: C  413 GLU cc_start: 0.8567 (tp30) cc_final: 0.8321 (tp30)
REVERT: H   35 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8192 (mp10)
REVERT: H   91 ASP cc_start: 0.8062 (t70) cc_final: 0.7438 (t70)
REVERT: H  105 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7985 (mm-40)
  outliers start: 17
  outliers final: 4
  residues processed: 107
  average time/residue: 1.2715
  time to fit residues: 142.1134
Evaluate side-chains
  101 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain H residue   35 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0770
   chunk 6 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0970
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.111421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.080978 restraints weight = 8872.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.14
r_work: 0.2869 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5867  Z= 0.201
  Angle     :  0.500   6.307   7914  Z= 0.266
  Chirality :  0.042   0.184    856
  Planarity :  0.004   0.056   1015
  Dihedral  :  9.452  68.338    919
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.26 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.31), residues: 748
  helix:  2.86 (0.26), residues: 377
  sheet:  0.17 (0.43), residues: 144
  loop : -0.08 (0.43), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  66 
 HIS   0.003   0.001   HIS A  33 
 PHE   0.011   0.001   PHE A  18 
 TYR   0.011   0.001   TYR H 117 
 ARG   0.002   0.000   ARG L  44 

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.586 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8259 (tt0) cc_final: 0.7567 (tm-30)
REVERT: A   89 TRP cc_start: 0.5572 (m-90) cc_final: 0.5307 (m-90)
REVERT: A  109 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7031 (mtm-85)
REVERT: A  131 MET cc_start: 0.8056 (tmm) cc_final: 0.7154 (mmp)
REVERT: B  144 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7690 (tpm-80)
REVERT: C  157 LYS cc_start: 0.8516 (mptt) cc_final: 0.8150 (mptp)
REVERT: C  413 GLU cc_start: 0.8607 (tp30) cc_final: 0.8364 (tp30)
REVERT: L  117 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8616 (pt0)
REVERT: H   91 ASP cc_start: 0.8029 (t70) cc_final: 0.7457 (t70)
REVERT: H  105 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7971 (mm-40)
  outliers start: 18
  outliers final: 7
  residues processed: 112
  average time/residue: 1.3177
  time to fit residues: 153.7762
Evaluate side-chains
  108 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   80 LYS
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain L residue   50 ASP
Chi-restraints excluded: chain L residue  117 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 57 optimal weight:    0.3980
   chunk 62 optimal weight:    0.4980
   chunk 70 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 64 optimal weight:    0.4980
   chunk 73 optimal weight:    0.2980
   chunk 25 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
C 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.111597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.081250 restraints weight = 8772.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 2.12
r_work: 0.2878 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5867  Z= 0.196
  Angle     :  0.485   5.862   7914  Z= 0.258
  Chirality :  0.041   0.154    856
  Planarity :  0.004   0.051   1015
  Dihedral  :  9.158  68.171    919
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.06 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.31), residues: 748
  helix:  2.96 (0.26), residues: 377
  sheet:  0.29 (0.43), residues: 144
  loop : -0.02 (0.43), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  66 
 HIS   0.003   0.001   HIS A  33 
 PHE   0.011   0.001   PHE A  18 
 TYR   0.011   0.001   TYR H 117 
 ARG   0.002   0.000   ARG L  44 

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8263 (tt0) cc_final: 0.7577 (tm-30)
REVERT: A   89 TRP cc_start: 0.5639 (m-90) cc_final: 0.5343 (m-90)
REVERT: A  109 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7031 (mtm-85)
REVERT: A  131 MET cc_start: 0.8066 (tmm) cc_final: 0.7157 (mmp)
REVERT: B  144 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7712 (tpm-80)
REVERT: C  157 LYS cc_start: 0.8507 (mptt) cc_final: 0.8157 (mptp)
REVERT: C  331 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8147 (mp)
REVERT: C  413 GLU cc_start: 0.8599 (tp30) cc_final: 0.8352 (tp30)
REVERT: H   91 ASP cc_start: 0.7999 (t70) cc_final: 0.7269 (t70)
REVERT: H  105 GLN cc_start: 0.8267 (mm-40) cc_final: 0.8030 (mm-40)
  outliers start: 15
  outliers final: 4
  residues processed: 109
  average time/residue: 1.5608
  time to fit residues: 177.6711
Evaluate side-chains
  106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain C residue  331 ILE
Chi-restraints excluded: chain L residue   33 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.109769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.079145 restraints weight = 8851.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.14
r_work: 0.2846 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5867  Z= 0.290
  Angle     :  0.530   6.667   7914  Z= 0.280
  Chirality :  0.042   0.153    856
  Planarity :  0.004   0.050   1015
  Dihedral  :  9.387  68.024    919
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 17.95 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.31), residues: 748
  helix:  2.92 (0.25), residues: 379
  sheet:  0.34 (0.44), residues: 137
  loop : -0.06 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  66 
 HIS   0.004   0.001   HIS H  54 
 PHE   0.011   0.001   PHE C 322 
 TYR   0.014   0.001   TYR H 117 
 ARG   0.002   0.000   ARG A 109 

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8328 (tt0) cc_final: 0.7549 (tm-30)
REVERT: A   89 TRP cc_start: 0.5573 (m-90) cc_final: 0.5303 (m-90)
REVERT: A  131 MET cc_start: 0.8072 (tmm) cc_final: 0.7160 (mmp)
REVERT: B  144 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7636 (tpm-80)
REVERT: C  157 LYS cc_start: 0.8469 (mptt) cc_final: 0.8102 (mptp)
REVERT: C  331 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8071 (mp)
REVERT: H   35 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8190 (mp10)
REVERT: H   91 ASP cc_start: 0.8005 (t70) cc_final: 0.7341 (t70)
  outliers start: 19
  outliers final: 8
  residues processed: 109
  average time/residue: 1.3619
  time to fit residues: 154.6341
Evaluate side-chains
  107 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain C residue  331 ILE
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   65 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0770
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
C 179 GLN

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 = 0.110328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.079958 restraints weight = 8733.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.12
r_work: 0.2856 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5867  Z= 0.238
  Angle     :  0.512   7.325   7914  Z= 0.271
  Chirality :  0.041   0.147    856
  Planarity :  0.004   0.049   1015
  Dihedral  :  9.312  68.251    919
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.21 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.31), residues: 748
  helix:  2.97 (0.25), residues: 379
  sheet:  0.24 (0.43), residues: 144
  loop :  0.00 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  66 
 HIS   0.004   0.001   HIS B 173 
 PHE   0.011   0.001   PHE C 322 
 TYR   0.012   0.001   TYR H 117 
 ARG   0.002   0.000   ARG C 272 

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.634 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8320 (tt0) cc_final: 0.7545 (tm-30)
REVERT: A   89 TRP cc_start: 0.5566 (m-90) cc_final: 0.5257 (m-90)
REVERT: A  131 MET cc_start: 0.8082 (tmm) cc_final: 0.7196 (mmp)
REVERT: B  144 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7622 (tpm-80)
REVERT: C  157 LYS cc_start: 0.8473 (mptt) cc_final: 0.8095 (mptp)
REVERT: C  331 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8097 (mp)
REVERT: H   35 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8171 (mp10)
REVERT: H   91 ASP cc_start: 0.7974 (t70) cc_final: 0.7240 (t70)
  outliers start: 16
  outliers final: 6
  residues processed: 104
  average time/residue: 1.2343
  time to fit residues: 134.2110
Evaluate side-chains
  105 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain C residue  331 ILE
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   65 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    0.1980
   chunk 65 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 44 optimal weight:    0.2980
   chunk 0 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.110754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.080333 restraints weight = 8756.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.12
r_work: 0.2864 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5867  Z= 0.222
  Angle     :  0.515   7.915   7914  Z= 0.273
  Chirality :  0.041   0.143    856
  Planarity :  0.004   0.049   1015
  Dihedral  :  9.219  68.376    919
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 20.47 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.31), residues: 748
  helix:  2.99 (0.25), residues: 379
  sheet:  0.30 (0.43), residues: 144
  loop :  0.00 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  54 
 PHE   0.011   0.001   PHE C 322 
 TYR   0.012   0.001   TYR H 117 
 ARG   0.001   0.000   ARG A 109 

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8267 (tt0) cc_final: 0.7525 (tm-30)
REVERT: A   89 TRP cc_start: 0.5878 (m-90) cc_final: 0.5578 (m-90)
REVERT: A  131 MET cc_start: 0.8047 (tmm) cc_final: 0.7185 (mmp)
REVERT: B  144 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7629 (tpm-80)
REVERT: B  184 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8288 (tt)
REVERT: C  151 ARG cc_start: 0.7448 (mtp85) cc_final: 0.6956 (ptp90)
REVERT: C  157 LYS cc_start: 0.8455 (mptt) cc_final: 0.8082 (mptp)
REVERT: C  331 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8087 (mp)
REVERT: H   35 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8185 (mp10)
REVERT: H   91 ASP cc_start: 0.7969 (t70) cc_final: 0.7230 (t70)
  outliers start: 11
  outliers final: 7
  residues processed: 103
  average time/residue: 1.2554
  time to fit residues: 135.1033
Evaluate side-chains
  107 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain C residue  331 ILE
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   65 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
C 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.110282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.079731 restraints weight = 8806.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.13
r_work: 0.2855 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5867  Z= 0.254
  Angle     :  0.521   8.449   7914  Z= 0.274
  Chirality :  0.042   0.149    856
  Planarity :  0.004   0.048   1015
  Dihedral  :  9.281  68.206    919
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 20.47 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.31), residues: 748
  helix:  2.98 (0.25), residues: 379
  sheet:  0.35 (0.43), residues: 137
  loop : -0.01 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  66 
 HIS   0.004   0.001   HIS H  54 
 PHE   0.011   0.001   PHE C 322 
 TYR   0.013   0.001   TYR H 117 
 ARG   0.001   0.000   ARG A 109 

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8261 (tt0) cc_final: 0.7523 (tm-30)
REVERT: A   89 TRP cc_start: 0.5975 (m-90) cc_final: 0.5666 (m-90)
REVERT: A  131 MET cc_start: 0.8080 (tmm) cc_final: 0.7215 (mmp)
REVERT: B  144 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7626 (tpm-80)
REVERT: B  184 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8314 (tt)
REVERT: C  151 ARG cc_start: 0.7447 (mtp85) cc_final: 0.6952 (ptp90)
REVERT: C  157 LYS cc_start: 0.8482 (mptt) cc_final: 0.8102 (mptp)
REVERT: C  331 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8093 (mp)
REVERT: H   35 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8177 (mp10)
REVERT: H   91 ASP cc_start: 0.7973 (t70) cc_final: 0.7281 (t70)
  outliers start: 10
  outliers final: 6
  residues processed: 105
  average time/residue: 1.3746
  time to fit residues: 150.8810
Evaluate side-chains
  107 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  144 ARG
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain C residue  331 ILE
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain H residue   35 GLN
Chi-restraints excluded: chain H residue   65 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 24 optimal weight:    0.3980
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.110503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.080071 restraints weight = 8767.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.12
r_work: 0.2846 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5867  Z= 0.239
  Angle     :  0.534   8.444   7914  Z= 0.280
  Chirality :  0.042   0.148    856
  Planarity :  0.004   0.049   1015
  Dihedral  :  9.257  68.290    919
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 20.65 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.31), residues: 748
  helix:  2.97 (0.25), residues: 379
  sheet:  0.30 (0.43), residues: 144
  loop :  0.02 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  54 
 PHE   0.011   0.001   PHE C 322 
 TYR   0.012   0.001   TYR H 117 
 ARG   0.015   0.000   ARG B 170 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5032.26 seconds
wall clock time: 86 minutes 17.18 seconds (5177.18 seconds total)