Starting phenix.real_space_refine
on Fri Aug 22 17:33:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8scx_40346/08_2025/8scx_40346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8scx_40346/08_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_40346/08_2025/8scx_40346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8scx_40346/08_2025/8scx_40346.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8scx_40346/08_2025/8scx_40346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8scx_40346/08_2025/8scx_40346.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 10, 'HIS:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1}
          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: 1.61, per 1000 atoms: 0.28
  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: 0.46
  Conformation dependent library (CDL) restraints added in 299.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.17
  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: 1.11

  Time building geometry restraints manager: 0.60 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:             3.300
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.510
  Find NCS groups from input model:        0.040
  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:9.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.010
-------------------------------------------------------------------------------
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   5870  Z= 0.334
  Angle     :  0.710   9.828   7920  Z= 0.380
  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 : 5.65
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (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
 ARG   0.002   0.000   ARG H 116 
 TYR   0.013   0.001   TYR H 117 
 PHE   0.008   0.001   PHE L  95 
 TRP   0.014   0.001   TRP H  66 
 HIS   0.004   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 ( 5867)
  covalent geometry    : angle       0.70440 ( 7914)
  SS BOND              : bond        0.00258 (    3)
  SS BOND              : angle       3.34137 (    6)
  hydrogen bonds       : bond        0.21156 (  384)
  hydrogen bonds       : angle       7.61792 ( 1146)

*********************** 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  : 0.226 
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: 0.5355
  time to fit residues: 66.9515
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  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.110053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.079661 restraints weight = 8996.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.14
r_work: 0.2844 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5870  Z= 0.187
  Angle     :  0.548   5.291   7920  Z= 0.292
  Chirality :  0.042   0.135    856
  Planarity :  0.004   0.044   1015
  Dihedral  : 10.286  79.195    919
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 10.05 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.31), residues: 748
  helix:  2.48 (0.25), residues: 375
  sheet:  0.13 (0.44), residues: 144
  loop : -0.05 (0.43), residues: 229

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 5867)
  covalent geometry    : angle       0.54494 ( 7914)
  SS BOND              : bond        0.00322 (    3)
  SS BOND              : angle       2.02074 (    6)
  hydrogen bonds       : bond        0.04399 (  384)
  hydrogen bonds       : angle       4.59647 ( 1146)

*********************** 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
  115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  131 MET cc_start: 0.8077 (tmm) cc_final: 0.6998 (mmp)
REVERT: B  144 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8369 (ttm-80)
REVERT: C  157 LYS cc_start: 0.8522 (mptt) cc_final: 0.8222 (mptp)
REVERT: C  413 GLU cc_start: 0.8614 (tp30) cc_final: 0.8409 (tp30)
REVERT: H   35 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8239 (mp10)
REVERT: H  105 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7965 (mm-40)
  outliers start: 15
  outliers final: 4
  residues processed: 107
  average time/residue: 0.4998
  time to fit residues: 55.7465
Evaluate side-chains
  99 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  144 ARG
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 51 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 36 optimal weight:    0.1980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.110973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.080619 restraints weight = 8910.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 2.13
r_work: 0.2870 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5870  Z= 0.149
  Angle     :  0.498   5.205   7920  Z= 0.264
  Chirality :  0.041   0.132    856
  Planarity :  0.004   0.040   1015
  Dihedral  :  9.365  72.843    919
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 13.82 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.32), residues: 748
  helix:  2.84 (0.26), residues: 377
  sheet:  0.19 (0.44), residues: 144
  loop : -0.07 (0.43), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  44 
 TYR   0.013   0.001   TYR H 117 
 PHE   0.011   0.001   PHE C 322 
 TRP   0.010   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5867)
  covalent geometry    : angle       0.49736 ( 7914)
  SS BOND              : bond        0.00276 (    3)
  SS BOND              : angle       1.18520 (    6)
  hydrogen bonds       : bond        0.03828 (  384)
  hydrogen bonds       : angle       4.10701 ( 1146)

*********************** 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
  122 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8291 (tt0) cc_final: 0.7554 (tm-30)
REVERT: A  109 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6947 (mtm-85)
REVERT: A  131 MET cc_start: 0.8021 (tmm) cc_final: 0.7116 (mmp)
REVERT: B  144 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8301 (ttm-80)
REVERT: C  157 LYS cc_start: 0.8496 (mptt) cc_final: 0.8167 (mptp)
REVERT: C  413 GLU cc_start: 0.8632 (tp30) cc_final: 0.8385 (tp30)
REVERT: H   91 ASP cc_start: 0.7987 (t70) cc_final: 0.7688 (t70)
REVERT: H  105 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7947 (mm-40)
  outliers start: 17
  outliers final: 5
  residues processed: 112
  average time/residue: 0.5549
  time to fit residues: 64.5679
Evaluate side-chains
  104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
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 L residue   33 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   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
C 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.110880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.080518 restraints weight = 8978.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 2.13
r_work: 0.2866 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5870  Z= 0.148
  Angle     :  0.483   5.206   7920  Z= 0.256
  Chirality :  0.041   0.131    856
  Planarity :  0.004   0.041   1015
  Dihedral  :  9.199  70.031    919
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 14.90 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.32), residues: 748
  helix:  2.95 (0.26), residues: 377
  sheet:  0.24 (0.43), residues: 144
  loop : -0.02 (0.43), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  44 
 TYR   0.012   0.001   TYR H 117 
 PHE   0.011   0.001   PHE A  18 
 TRP   0.011   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 5867)
  covalent geometry    : angle       0.48275 ( 7914)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       0.90400 (    6)
  hydrogen bonds       : bond        0.03578 (  384)
  hydrogen bonds       : angle       4.00668 ( 1146)

*********************** 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
  120 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8278 (tt0) cc_final: 0.7538 (tm-30)
REVERT: A  109 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6984 (mtm-85)
REVERT: A  131 MET cc_start: 0.8057 (tmm) cc_final: 0.7123 (mmp)
REVERT: B  144 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8315 (ttm-80)
REVERT: C  157 LYS cc_start: 0.8546 (mptt) cc_final: 0.8198 (mptp)
REVERT: C  413 GLU cc_start: 0.8575 (tp30) cc_final: 0.8334 (tp30)
REVERT: H   35 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8239 (mp10)
REVERT: H   91 ASP cc_start: 0.7939 (t70) cc_final: 0.7519 (t70)
REVERT: H  105 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7935 (mm-40)
  outliers start: 19
  outliers final: 4
  residues processed: 110
  average time/residue: 0.5275
  time to fit residues: 60.4026
Evaluate side-chains
  104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
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 21 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
C 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.110346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.079654 restraints weight = 9050.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 2.16
r_work: 0.2847 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5870  Z= 0.190
  Angle     :  0.530   7.567   7920  Z= 0.281
  Chirality :  0.043   0.191    856
  Planarity :  0.004   0.050   1015
  Dihedral  :  9.437  68.893    919
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 16.16 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.31), residues: 748
  helix:  2.88 (0.26), residues: 377
  sheet:  0.26 (0.43), residues: 144
  loop : -0.06 (0.43), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  44 
 TYR   0.014   0.001   TYR H 117 
 PHE   0.011   0.001   PHE C 322 
 TRP   0.013   0.001   TRP H  66 
 HIS   0.004   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 5867)
  covalent geometry    : angle       0.52316 ( 7914)
  SS BOND              : bond        0.00330 (    3)
  SS BOND              : angle       3.19617 (    6)
  hydrogen bonds       : bond        0.03751 (  384)
  hydrogen bonds       : angle       4.03872 ( 1146)

*********************** 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
  111 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8318 (tt0) cc_final: 0.7556 (tm-30)
REVERT: A  109 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7042 (mtm-85)
REVERT: A  131 MET cc_start: 0.8068 (tmm) cc_final: 0.7147 (mmp)
REVERT: B  144 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8341 (ttm-80)
REVERT: C  157 LYS cc_start: 0.8482 (mptt) cc_final: 0.8134 (mptp)
REVERT: C  413 GLU cc_start: 0.8613 (tp30) cc_final: 0.8372 (tp30)
REVERT: H   35 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8236 (mp10)
REVERT: H   91 ASP cc_start: 0.7975 (t70) cc_final: 0.7526 (t70)
  outliers start: 13
  outliers final: 5
  residues processed: 104
  average time/residue: 0.4956
  time to fit residues: 53.7297
Evaluate side-chains
  103 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
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 L residue   33 VAL
Chi-restraints excluded: chain H residue   35 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0370
   chunk 48 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
C 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.111815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.081391 restraints weight = 8889.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.13
r_work: 0.2879 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5870  Z= 0.133
  Angle     :  0.489   5.863   7920  Z= 0.258
  Chirality :  0.041   0.150    856
  Planarity :  0.004   0.048   1015
  Dihedral  :  9.114  68.033    919
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.24 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.37 (0.31), residues: 748
  helix:  2.98 (0.25), residues: 377
  sheet:  0.36 (0.43), residues: 144
  loop : -0.04 (0.43), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  44 
 TYR   0.011   0.001   TYR H 117 
 PHE   0.010   0.001   PHE A  18 
 TRP   0.012   0.001   TRP H  66 
 HIS   0.003   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5867)
  covalent geometry    : angle       0.48615 ( 7914)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       2.10276 (    6)
  hydrogen bonds       : bond        0.03374 (  384)
  hydrogen bonds       : angle       3.89689 ( 1146)

*********************** 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
  115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8254 (tt0) cc_final: 0.7534 (tm-30)
REVERT: A  131 MET cc_start: 0.8042 (tmm) cc_final: 0.7150 (mmp)
REVERT: B  144 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8279 (ttm-80)
REVERT: C  157 LYS cc_start: 0.8496 (mptt) cc_final: 0.8242 (mptp)
REVERT: C  331 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8114 (mp)
REVERT: C  413 GLU cc_start: 0.8557 (tp30) cc_final: 0.8314 (tp30)
REVERT: H   35 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8200 (mp10)
REVERT: H   91 ASP cc_start: 0.7857 (t70) cc_final: 0.7368 (t70)
REVERT: H  101 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8763 (mtp)
  outliers start: 13
  outliers final: 7
  residues processed: 107
  average time/residue: 0.4920
  time to fit residues: 54.9009
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  : 0.187 
-------------------------------------------------------------------------------
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 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
Chi-restraints excluded: chain H residue  101 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0050
   chunk 4 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
C 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.110801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.080342 restraints weight = 8869.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.13
r_work: 0.2868 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5870  Z= 0.160
  Angle     :  0.514   6.946   7920  Z= 0.270
  Chirality :  0.041   0.150    856
  Planarity :  0.004   0.048   1015
  Dihedral  :  9.157  67.951    919
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 16.34 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.31), residues: 748
  helix:  3.02 (0.25), residues: 378
  sheet:  0.38 (0.43), residues: 144
  loop : -0.01 (0.43), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 144 
 TYR   0.013   0.001   TYR H 117 
 PHE   0.010   0.001   PHE C 322 
 TRP   0.012   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 5867)
  covalent geometry    : angle       0.51109 ( 7914)
  SS BOND              : bond        0.00305 (    3)
  SS BOND              : angle       1.92507 (    6)
  hydrogen bonds       : bond        0.03463 (  384)
  hydrogen bonds       : angle       3.89203 ( 1146)

*********************** 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
  117 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8281 (tt0) cc_final: 0.7528 (tm-30)
REVERT: A  131 MET cc_start: 0.8052 (tmm) cc_final: 0.7155 (mmp)
REVERT: B  144 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8273 (ttm-80)
REVERT: C  157 LYS cc_start: 0.8465 (mptt) cc_final: 0.8114 (mptp)
REVERT: C  331 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8129 (mp)
REVERT: C  413 GLU cc_start: 0.8543 (tp30) cc_final: 0.8288 (tp30)
REVERT: H   35 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8189 (mp10)
REVERT: H   91 ASP cc_start: 0.7846 (t70) cc_final: 0.7372 (t70)
REVERT: H  101 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8778 (mtp)
  outliers start: 18
  outliers final: 8
  residues processed: 107
  average time/residue: 0.4787
  time to fit residues: 53.4614
Evaluate side-chains
  107 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
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   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 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
Chi-restraints excluded: chain H residue  101 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 56 optimal weight:    0.1980
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.111256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.080949 restraints weight = 8853.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 2.12
r_work: 0.2878 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5870  Z= 0.140
  Angle     :  0.498   7.321   7920  Z= 0.262
  Chirality :  0.041   0.143    856
  Planarity :  0.004   0.048   1015
  Dihedral  :  8.889  68.301    919
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.59 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.31), residues: 748
  helix:  3.05 (0.25), residues: 379
  sheet:  0.40 (0.43), residues: 144
  loop :  0.04 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 272 
 TYR   0.012   0.001   TYR H 117 
 PHE   0.010   0.001   PHE A  96 
 TRP   0.012   0.001   TRP H  66 
 HIS   0.003   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5867)
  covalent geometry    : angle       0.49622 ( 7914)
  SS BOND              : bond        0.00276 (    3)
  SS BOND              : angle       1.70407 (    6)
  hydrogen bonds       : bond        0.03340 (  384)
  hydrogen bonds       : angle       3.86882 ( 1146)

*********************** 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
  116 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8344 (tt0) cc_final: 0.7565 (tm-30)
REVERT: A  131 MET cc_start: 0.8068 (tmm) cc_final: 0.7200 (mmp)
REVERT: B  144 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8272 (ttm-80)
REVERT: C  157 LYS cc_start: 0.8469 (mptt) cc_final: 0.8113 (mptp)
REVERT: C  331 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8122 (mp)
REVERT: C  413 GLU cc_start: 0.8562 (tp30) cc_final: 0.8311 (tp30)
REVERT: H   35 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8179 (mp10)
REVERT: H   91 ASP cc_start: 0.7833 (t70) cc_final: 0.7323 (t70)
REVERT: H  101 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8752 (mtp)
  outliers start: 15
  outliers final: 6
  residues processed: 107
  average time/residue: 0.4552
  time to fit residues: 50.8804
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  : 0.142 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain H residue  101 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0040
   chunk 33 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.5192

-------------------------------------------------------------------------------
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
C 392 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.111384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.081092 restraints weight = 8906.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.13
r_work: 0.2881 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5870  Z= 0.137
  Angle     :  0.510   7.900   7920  Z= 0.268
  Chirality :  0.041   0.140    856
  Planarity :  0.004   0.048   1015
  Dihedral  :  8.729  68.330    919
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.49 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.31), residues: 748
  helix:  3.07 (0.25), residues: 379
  sheet:  0.51 (0.43), residues: 137
  loop :  0.03 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 144 
 TYR   0.011   0.001   TYR H 117 
 PHE   0.010   0.001   PHE A  96 
 TRP   0.012   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5867)
  covalent geometry    : angle       0.50777 ( 7914)
  SS BOND              : bond        0.00269 (    3)
  SS BOND              : angle       1.63515 (    6)
  hydrogen bonds       : bond        0.03319 (  384)
  hydrogen bonds       : angle       3.80969 ( 1146)

*********************** 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
  114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8356 (tt0) cc_final: 0.7595 (tm-30)
REVERT: A  131 MET cc_start: 0.8029 (tmm) cc_final: 0.7210 (mmp)
REVERT: B  144 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8267 (ttm-80)
REVERT: C  151 ARG cc_start: 0.7451 (mtp85) cc_final: 0.7011 (ptp90)
REVERT: C  157 LYS cc_start: 0.8472 (mptt) cc_final: 0.8112 (mptp)
REVERT: C  331 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8136 (mp)
REVERT: C  413 GLU cc_start: 0.8566 (tp30) cc_final: 0.8308 (tp30)
REVERT: H   35 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8186 (mp10)
REVERT: H   91 ASP cc_start: 0.7807 (t70) cc_final: 0.7291 (t70)
REVERT: H  101 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8761 (mtp)
  outliers start: 13
  outliers final: 7
  residues processed: 108
  average time/residue: 0.4689
  time to fit residues: 52.6916
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  : 0.180 
-------------------------------------------------------------------------------
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 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
Chi-restraints excluded: chain H residue  101 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 42 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
C 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.110847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.080491 restraints weight = 8866.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.12
r_work: 0.2866 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5870  Z= 0.155
  Angle     :  0.514   8.468   7920  Z= 0.269
  Chirality :  0.041   0.149    856
  Planarity :  0.004   0.047   1015
  Dihedral  :  8.763  68.301    919
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.49 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.51 (0.31), residues: 748
  helix:  3.05 (0.25), residues: 379
  sheet:  0.50 (0.43), residues: 137
  loop :  0.04 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 144 
 TYR   0.012   0.001   TYR H 117 
 PHE   0.010   0.001   PHE A  96 
 TRP   0.012   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5867)
  covalent geometry    : angle       0.51170 ( 7914)
  SS BOND              : bond        0.00311 (    3)
  SS BOND              : angle       1.73883 (    6)
  hydrogen bonds       : bond        0.03376 (  384)
  hydrogen bonds       : angle       3.85075 ( 1146)

********************** 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
  114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A   86 GLU cc_start: 0.8370 (tt0) cc_final: 0.7602 (tm-30)
REVERT: A  131 MET cc_start: 0.8018 (tmm) cc_final: 0.7207 (mmp)
REVERT: B  144 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8252 (ttm-80)
REVERT: C  151 ARG cc_start: 0.7400 (mtp85) cc_final: 0.6987 (ptp90)
REVERT: C  157 LYS cc_start: 0.8462 (mptt) cc_final: 0.8102 (mptp)
REVERT: C  331 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8125 (mp)
REVERT: C  413 GLU cc_start: 0.8558 (tp30) cc_final: 0.8306 (tp30)
REVERT: H   35 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8179 (mp10)
REVERT: H   91 ASP cc_start: 0.7787 (t70) cc_final: 0.7266 (t70)
REVERT: H  101 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8755 (mtp)
REVERT: H  105 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7884 (mm-40)
  outliers start: 12
  outliers final: 7
  residues processed: 106
  average time/residue: 0.4911
  time to fit residues: 54.2451
Evaluate side-chains
  110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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 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
Chi-restraints excluded: chain H residue  101 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 30 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:   30.0000
   chunk 44 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0010
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.6790

-------------------------------------------------------------------------------
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
C 392 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.110846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.080266 restraints weight = 8815.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.13
r_work: 0.2866 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5870  Z= 0.159
  Angle     :  0.528   8.421   7920  Z= 0.276
  Chirality :  0.042   0.149    856
  Planarity :  0.004   0.047   1015
  Dihedral  :  8.760  68.276    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 :  2.33 %
    Allowed  : 18.13 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.31), residues: 748
  helix:  3.04 (0.25), residues: 379
  sheet:  0.49 (0.43), residues: 137
  loop :  0.02 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  83 
 TYR   0.012   0.001   TYR H 117 
 PHE   0.010   0.001   PHE A  96 
 TRP   0.013   0.001   TRP H  66 
 HIS   0.003   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 5867)
  covalent geometry    : angle       0.52644 ( 7914)
  SS BOND              : bond        0.00306 (    3)
  SS BOND              : angle       1.71596 (    6)
  hydrogen bonds       : bond        0.03399 (  384)
  hydrogen bonds       : angle       3.84620 ( 1146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2149.61 seconds
wall clock time: 37 minutes 14.86 seconds (2234.86 seconds total)