Starting phenix.real_space_refine
on Fri Jul 25 14:01:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sp9_25369/07_2025/7sp9_25369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sp9_25369/07_2025/7sp9_25369.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sp9_25369/07_2025/7sp9_25369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sp9_25369/07_2025/7sp9_25369.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sp9_25369/07_2025/7sp9_25369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sp9_25369/07_2025/7sp9_25369.cif"
  }
  resolution = 2.9
  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=  -0.001 sd=   0.828
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1816 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    3857      2.51       5
     N     984      2.21       5
     O    1090      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5966
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 944
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
    Chain: "C"
      Number of atoms: 918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 918
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 2, 'TRANS': 114}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 4054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4054
          Classifications: {'peptide': 497}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 483}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 50
          Unusual residues: {'NAG': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.35, per 1000 atoms: 0.73
  Number of scatterers: 5966
  At special positions: 0
  Unit cell: (70.2, 71.28, 154.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O    1090      8.00
     N     984      7.00
     C    3857      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " 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: 1.47
  Conformation dependent library (CDL) restraints added in 877.9 milliseconds
  

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1366

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 7 sheets defined
      48.8% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.889A  pdb=" N   THR B  31 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 65
      removed outlier: 3.616A  pdb=" N   GLY B  65 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 62 through 65'
    Processing helix  chain 'B' and resid 86 through 90
    Processing helix  chain 'B' and resid 107 through 111
      removed outlier: 3.541A  pdb=" N   TYR B 111 " --> pdb=" O   THR B 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.620A  pdb=" N   THR C  90 " --> pdb=" O   PRO C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 113
    Processing helix  chain 'A' and resid 39 through 74
      removed outlier: 3.625A  pdb=" N   LEU A  74 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 107
    Processing helix  chain 'A' and resid 127 through 138
      removed outlier: 3.970A  pdb=" N   ALA A 131 " --> pdb=" O   ASP A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 156 through 160
      removed outlier: 3.559A  pdb=" N   THR A 159 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 190
    Processing helix  chain 'A' and resid 209 through 221
      Proline residue:  A 217  - end of helix
      removed outlier: 3.899A  pdb=" N   CYS A 220 " --> pdb=" O   TYR A 216 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ASP A 221 " --> pdb=" O   PRO A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 262
      removed outlier: 4.044A  pdb=" N   ARG A 256 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLY A 257 " --> pdb=" O   ASN A 253 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TRP A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 290
      removed outlier: 5.259A  pdb=" N   ASP A 285 " --> pdb=" O   ASN A 281 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
      removed outlier: 3.514A  pdb=" N   GLN A 290 " --> pdb=" O   PRO A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 312
      removed outlier: 3.804A  pdb=" N   LEU A 305 " --> pdb=" O   ASP A 301 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   THR A 306 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ARG A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 356
      removed outlier: 5.267A  pdb=" N   TRP A 351 " --> pdb=" O   CYS A 347 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   TYR A 352 " --> pdb=" O   ARG A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 392
      removed outlier: 4.068A  pdb=" N   ALA A 368 " --> pdb=" O   GLY A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 420
    Processing helix  chain 'A' and resid 421 through 428
      removed outlier: 3.616A  pdb=" N   ALA A 424 " --> pdb=" O   ASN A 421 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   PHE A 425 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 428 " --> pdb=" O   PHE A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 449
      removed outlier: 3.834A  pdb=" N   VAL A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ILE A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      Proline residue:  A 440  - end of helix
      removed outlier: 3.519A  pdb=" N   MET A 449 " --> pdb=" O   ALA A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 497
    Processing helix  chain 'A' and resid 504 through 535
      removed outlier: 3.708A  pdb=" N   ILE A 533 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 552
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.572A  pdb=" N   SER B  21 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL B  20 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12
      removed outlier: 5.557A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   SER B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12
      removed outlier: 5.557A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 101
    Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.744A  pdb=" N   LEU C  18 " --> pdb=" O   MET C  82 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU C  20 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 52
      removed outlier: 4.005A  pdb=" N   ALA C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU C  34 " --> pdb=" O   SER C  51 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   TYR C 115 " --> pdb=" O   LEU C  97 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 142 through 143
      removed outlier: 8.625A  pdb=" N   ILE A 168 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LEU A 116 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ILE A 170 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   CYS A 118 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   GLN A 172 " --> pdb=" O   CYS A 118 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   ILE A 120 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   VAL A  84 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ARG A 115 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLY A  90 " --> pdb=" O   VAL A 119 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASP A 121 " --> pdb=" O   GLY A  90 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ALA A  85 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   ILE A 200 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   ILE A  87 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   LEU A 272 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   LYS A 225 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   ILE A 224 " --> pdb=" O   ILE A 316 " (cutoff:3.500A)
      removed outlier: 10.398A  pdb=" N   TYR A 318 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 10.615A  pdb=" N   ALA A 226 " --> pdb=" O   TYR A 318 " (cutoff:3.500A)
      removed outlier: 10.219A  pdb=" N   ALA A 228 " --> pdb=" O   PRO A 320 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ALA A 322 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)

    316 hydrogen bonds defined for protein.
    873 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: 1.94

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1071
        1.33 -     1.45: 1716
        1.45 -     1.57: 3260
        1.57 -     1.69: 16
        1.69 -     1.81: 53
  Bond restraints: 6116
  Sorted by residual:
  bond pdb=" CBD Y01 A 902 "
       pdb=" CBG Y01 A 902 "
    ideal  model  delta    sigma   weight residual
    1.520  1.643 -0.123 2.00e-02 2.50e+03 3.81e+01
  bond pdb=" CAV Y01 A 902 "
       pdb=" CAZ Y01 A 902 "
    ideal  model  delta    sigma   weight residual
    1.507  1.612 -0.105 2.00e-02 2.50e+03 2.73e+01
  bond pdb=" CAV Y01 A 902 "
       pdb=" CBC Y01 A 902 "
    ideal  model  delta    sigma   weight residual
    1.523  1.616 -0.093 2.00e-02 2.50e+03 2.17e+01
  bond pdb=" CAY Y01 A 902 "
       pdb=" OAW Y01 A 902 "
    ideal  model  delta    sigma   weight residual
    1.332  1.423 -0.091 2.00e-02 2.50e+03 2.06e+01
  bond pdb=" CBF Y01 A 902 "
       pdb=" CBH Y01 A 902 "
    ideal  model  delta    sigma   weight residual
    1.550  1.638 -0.088 2.00e-02 2.50e+03 1.95e+01
  ... (remaining 6111 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 8239
        2.62 -     5.24: 45
        5.24 -     7.87: 14
        7.87 -    10.49: 1
       10.49 -    13.11: 3
  Bond angle restraints: 8302
  Sorted by residual:
  angle pdb=" CAM Y01 A 902 "
        pdb=" CAY Y01 A 902 "
        pdb=" OAW Y01 A 902 "
      ideal   model   delta    sigma   weight residual
     111.19  124.30  -13.11 3.00e+00 1.11e-01 1.91e+01
  angle pdb=" CAI Y01 A 902 "
        pdb=" CAZ Y01 A 902 "
        pdb=" CAV Y01 A 902 "
      ideal   model   delta    sigma   weight residual
     120.03  131.83  -11.80 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" CAZ Y01 A 902 "
        pdb=" CAV Y01 A 902 "
        pdb=" CBC Y01 A 902 "
      ideal   model   delta    sigma   weight residual
     111.19  122.91  -11.72 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" CAV Y01 A 902 "
        pdb=" CAZ Y01 A 902 "
        pdb=" CBH Y01 A 902 "
      ideal   model   delta    sigma   weight residual
     116.96  108.74    8.22 3.00e+00 1.11e-01 7.50e+00
  angle pdb=" C   VAL A 254 "
        pdb=" N   GLU A 255 "
        pdb=" CA  GLU A 255 "
      ideal   model   delta    sigma   weight residual
     120.44  116.76    3.68 1.36e+00 5.41e-01 7.31e+00
  ... (remaining 8297 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.23: 3334
       16.23 -    32.47: 207
       32.47 -    48.70: 48
       48.70 -    64.93: 13
       64.93 -    81.16: 5
  Dihedral angle restraints: 3607
    sinusoidal: 1461
      harmonic: 2146
  Sorted by residual:
  dihedral pdb=" CB  MET A 382 "
           pdb=" CG  MET A 382 "
           pdb=" SD  MET A 382 "
           pdb=" CE  MET A 382 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.24   51.24     3      1.50e+01 4.44e-03 8.99e+00
  dihedral pdb=" CA  LEU A 293 "
           pdb=" CB  LEU A 293 "
           pdb=" CG  LEU A 293 "
           pdb=" CD1 LEU A 293 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  104.68  -44.68     3      1.50e+01 4.44e-03 8.04e+00
  dihedral pdb=" CA  ARG A 334 "
           pdb=" CB  ARG A 334 "
           pdb=" CG  ARG A 334 "
           pdb=" CD  ARG A 334 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.28  -42.72     3      1.50e+01 4.44e-03 7.67e+00
  ... (remaining 3604 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 838
       0.080 -    0.159: 63
       0.159 -    0.239: 2
       0.239 -    0.319: 1
       0.319 -    0.398: 3
  Chirality restraints: 907
  Sorted by residual:
  chirality pdb=" CBG Y01 A 902 "
            pdb=" CAQ Y01 A 902 "
            pdb=" CBD Y01 A 902 "
            pdb=" CBI Y01 A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.73    0.40 2.00e-01 2.50e+01 3.97e+00
  chirality pdb=" CBE Y01 A 902 "
            pdb=" CAP Y01 A 902 "
            pdb=" CBB Y01 A 902 "
            pdb=" CBI Y01 A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.93   -0.36 2.00e-01 2.50e+01 3.29e+00
  chirality pdb=" CBI Y01 A 902 "
            pdb=" CAU Y01 A 902 "
            pdb=" CBE Y01 A 902 "
            pdb=" CBG Y01 A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94    2.61    0.33 2.00e-01 2.50e+01 2.67e+00
  ... (remaining 904 not shown)

  Planarity restraints: 1026
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  94 "    0.019 5.00e-02 4.00e+02   2.90e-02 1.35e+00
        pdb=" N   PRO A  95 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 346 "   -0.009 2.00e-02 2.50e+03   7.12e-03 1.27e+00
        pdb=" CG  TRP A 346 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 346 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 346 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 346 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 346 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 346 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 346 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 346 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 346 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 447 "   -0.006 2.00e-02 2.50e+03   8.45e-03 1.25e+00
        pdb=" CG  PHE A 447 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 447 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 447 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 447 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 447 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 447 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1023 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1081
        2.78 -     3.31: 5704
        3.31 -     3.84: 9815
        3.84 -     4.37: 11047
        4.37 -     4.90: 19773
  Nonbonded interactions: 47420
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 499 "
            pdb=" OH  TYR A 507 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OH  TYR A  46 "
            pdb=" OAG Y01 A 902 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG  SER C  51 "
            pdb=" O   GLY C  56 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   THR A  82 "
            pdb=" OH  TYR A 110 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" NH2 ARG A  67 "
            pdb=" O   SER A 260 "
     model   vdw
     2.323 3.120
  ... (remaining 47415 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:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.400
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
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      :  0.004   0.123   6117  Z= 0.224
  Angle     :  0.568  13.110   8304  Z= 0.260
  Chirality :  0.046   0.398    907
  Planarity :  0.003   0.029   1026
  Dihedral  : 12.065  81.163   2238
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.62 (0.31), residues: 725
  helix:  2.16 (0.29), residues: 315
  sheet:  1.47 (0.44), residues: 150
  loop : -0.55 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 552 
 PHE   0.019   0.001   PHE A 447 
 TYR   0.013   0.001   TYR A 414 
 ARG   0.005   0.000   ARG A  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18663 (  312)
  hydrogen bonds       : angle       6.48689 (  873)
  SS BOND              : bond        0.00293 (    1)
  SS BOND              : angle       0.15093 (    2)
  covalent geometry    : bond        0.00442 ( 6116)
  covalent geometry    : angle       0.56784 ( 8302)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.595 
Fit side-chains
REVERT: A  348 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7349 (ptp90)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 1.0488
  time to fit residues: 137.4399
Evaluate side-chains
  88 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.106552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.093671 restraints weight = 12328.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.06
r_work: 0.3262 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6117  Z= 0.184
  Angle     :  0.608   8.568   8304  Z= 0.316
  Chirality :  0.043   0.131    907
  Planarity :  0.004   0.042   1026
  Dihedral  :  5.440  52.736    917
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.34 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.26 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.30 (0.30), residues: 725
  helix:  2.03 (0.29), residues: 311
  sheet:  1.14 (0.42), residues: 151
  loop : -0.75 (0.35), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 262 
 HIS   0.002   0.001   HIS A 174 
 PHE   0.018   0.002   PHE A  49 
 TYR   0.015   0.002   TYR A 528 
 ARG   0.006   0.001   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  312)
  hydrogen bonds       : angle       4.42881 (  873)
  SS BOND              : bond        0.00451 (    1)
  SS BOND              : angle       0.94475 (    2)
  covalent geometry    : bond        0.00418 ( 6116)
  covalent geometry    : angle       0.60762 ( 8302)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.692 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.6627 (ttt-90)
REVERT: B   84 SER cc_start: 0.8005 (p) cc_final: 0.7669 (t)
REVERT: C   28 ILE cc_start: 0.7628 (pt) cc_final: 0.7379 (pt)
REVERT: A  248 TYR cc_start: 0.8222 (m-10) cc_final: 0.7873 (m-10)
REVERT: A  348 ARG cc_start: 0.8200 (mtm110) cc_final: 0.7797 (ptp90)
  outliers start: 14
  outliers final: 9
  residues processed: 107
  average time/residue: 0.9939
  time to fit residues: 112.3955
Evaluate side-chains
  85 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  552 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 63 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 116 GLN
A 253 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.104157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.091403 restraints weight = 12436.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.06
r_work: 0.3218 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6117  Z= 0.140
  Angle     :  0.528   8.472   8304  Z= 0.278
  Chirality :  0.042   0.144    907
  Planarity :  0.003   0.027   1026
  Dihedral  :  5.141  42.060    917
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.79 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 14.01 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.28 (0.30), residues: 725
  helix:  2.08 (0.29), residues: 312
  sheet:  0.97 (0.42), residues: 152
  loop : -0.75 (0.34), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 262 
 HIS   0.002   0.001   HIS A 174 
 PHE   0.014   0.001   PHE A 249 
 TYR   0.014   0.001   TYR A 430 
 ARG   0.007   0.001   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04125 (  312)
  hydrogen bonds       : angle       4.20144 (  873)
  SS BOND              : bond        0.00416 (    1)
  SS BOND              : angle       0.46474 (    2)
  covalent geometry    : bond        0.00314 ( 6116)
  covalent geometry    : angle       0.52776 ( 8302)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.625 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.6979 (ttm-80) cc_final: 0.6579 (ttt-90)
REVERT: A  253 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8311 (m-40)
REVERT: A  348 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7769 (ptp90)
REVERT: A  372 MET cc_start: 0.7890 (mtp) cc_final: 0.7618 (mtt)
REVERT: A  530 ILE cc_start: 0.9014 (tt) cc_final: 0.8531 (pt)
REVERT: A  547 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8328 (tp30)
  outliers start: 23
  outliers final: 15
  residues processed: 95
  average time/residue: 1.3054
  time to fit residues: 130.0182
Evaluate side-chains
  89 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  253 ASN
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  552 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.101309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.089121 restraints weight = 12756.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.01
r_work: 0.3216 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6117  Z= 0.172
  Angle     :  0.547   8.536   8304  Z= 0.295
  Chirality :  0.043   0.149    907
  Planarity :  0.004   0.038   1026
  Dihedral  :  4.942  37.930    917
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.62 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 14.97 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.16 (0.30), residues: 725
  helix:  1.99 (0.29), residues: 312
  sheet:  0.91 (0.42), residues: 152
  loop : -0.85 (0.34), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 246 
 HIS   0.001   0.001   HIS A 195 
 PHE   0.020   0.002   PHE A 252 
 TYR   0.014   0.001   TYR A 430 
 ARG   0.008   0.001   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04317 (  312)
  hydrogen bonds       : angle       4.18203 (  873)
  SS BOND              : bond        0.00329 (    1)
  SS BOND              : angle       0.44995 (    2)
  covalent geometry    : bond        0.00392 ( 6116)
  covalent geometry    : angle       0.54733 ( 8302)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 0.544 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6995 (ttt-90)
REVERT: B   84 SER cc_start: 0.8247 (p) cc_final: 0.7961 (t)
REVERT: A  348 ARG cc_start: 0.8219 (mtm110) cc_final: 0.7742 (ptp90)
REVERT: A  372 MET cc_start: 0.7932 (mtp) cc_final: 0.7660 (mtt)
  outliers start: 29
  outliers final: 15
  residues processed: 100
  average time/residue: 1.6901
  time to fit residues: 178.5325
Evaluate side-chains
  95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   66 ARG
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  552 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.100834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.088787 restraints weight = 12556.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 1.97
r_work: 0.3208 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.4075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6117  Z= 0.147
  Angle     :  0.533   8.999   8304  Z= 0.285
  Chirality :  0.042   0.153    907
  Planarity :  0.003   0.026   1026
  Dihedral  :  4.806  35.578    917
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.07 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 16.24 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.14 (0.30), residues: 725
  helix:  2.00 (0.29), residues: 312
  sheet:  0.85 (0.42), residues: 152
  loop : -0.86 (0.34), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 262 
 HIS   0.002   0.001   HIS A 195 
 PHE   0.013   0.001   PHE B  47 
 TYR   0.014   0.001   TYR A 430 
 ARG   0.005   0.001   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  312)
  hydrogen bonds       : angle       4.11613 (  873)
  SS BOND              : bond        0.00315 (    1)
  SS BOND              : angle       0.39161 (    2)
  covalent geometry    : bond        0.00333 ( 6116)
  covalent geometry    : angle       0.53280 ( 8302)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.714 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6836 (ttt-90)
REVERT: C   60 TYR cc_start: 0.8041 (m-80) cc_final: 0.7640 (m-80)
REVERT: A  348 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7691 (ttp80)
REVERT: A  372 MET cc_start: 0.7984 (mtp) cc_final: 0.7691 (mtt)
  outliers start: 22
  outliers final: 16
  residues processed: 96
  average time/residue: 1.1512
  time to fit residues: 116.4288
Evaluate side-chains
  93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   66 ARG
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   72 ASP
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  266 GLN
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  552 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 66 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0980
   chunk 60 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
A  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.099836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.088016 restraints weight = 12426.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.94
r_work: 0.3194 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6117  Z= 0.153
  Angle     :  0.541   7.487   8304  Z= 0.290
  Chirality :  0.042   0.156    907
  Planarity :  0.004   0.047   1026
  Dihedral  :  4.736  36.942    917
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.34 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 16.40 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.12 (0.30), residues: 725
  helix:  2.05 (0.29), residues: 312
  sheet:  0.78 (0.42), residues: 153
  loop : -0.91 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 246 
 HIS   0.001   0.001   HIS A 195 
 PHE   0.014   0.001   PHE B  47 
 TYR   0.015   0.001   TYR A 414 
 ARG   0.009   0.001   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  312)
  hydrogen bonds       : angle       4.07925 (  873)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       0.41875 (    2)
  covalent geometry    : bond        0.00347 ( 6116)
  covalent geometry    : angle       0.54094 ( 8302)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.744 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6907 (ttt-90)
REVERT: C    3 GLN cc_start: 0.8455 (mp10) cc_final: 0.8225 (mp10)
REVERT: A  348 ARG cc_start: 0.8276 (mtm110) cc_final: 0.7730 (ptp90)
REVERT: A  372 MET cc_start: 0.8009 (mtp) cc_final: 0.7711 (mtt)
  outliers start: 26
  outliers final: 17
  residues processed: 99
  average time/residue: 1.4733
  time to fit residues: 152.6569
Evaluate side-chains
  99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   66 ARG
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   60 TYR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  266 GLN
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  552 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 1 optimal weight:    0.0470
   chunk 59 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0980
   chunk 47 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.100833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.088827 restraints weight = 12574.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.97
r_work: 0.3210 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6117  Z= 0.122
  Angle     :  0.538   7.423   8304  Z= 0.284
  Chirality :  0.041   0.161    907
  Planarity :  0.003   0.028   1026
  Dihedral  :  4.604  36.982    917
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.07 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.15 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.19 (0.30), residues: 725
  helix:  2.12 (0.29), residues: 312
  sheet:  0.93 (0.42), residues: 145
  loop : -0.94 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 195 
 PHE   0.012   0.001   PHE A  49 
 TYR   0.015   0.001   TYR A 414 
 ARG   0.007   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  312)
  hydrogen bonds       : angle       4.02349 (  873)
  SS BOND              : bond        0.00337 (    1)
  SS BOND              : angle       0.45132 (    2)
  covalent geometry    : bond        0.00269 ( 6116)
  covalent geometry    : angle       0.53762 ( 8302)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.622 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6798 (ttt-90)
REVERT: C    3 GLN cc_start: 0.8473 (mp10) cc_final: 0.8227 (mp10)
REVERT: A  348 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7707 (ptp90)
REVERT: A  372 MET cc_start: 0.8000 (mtp) cc_final: 0.7749 (mtt)
  outliers start: 20
  outliers final: 11
  residues processed: 95
  average time/residue: 1.1777
  time to fit residues: 117.5492
Evaluate side-chains
  93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   66 ARG
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   60 TYR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  552 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
C  73 ASN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.097439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.085617 restraints weight = 12520.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.93
r_work: 0.3148 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6117  Z= 0.230
  Angle     :  0.620   7.492   8304  Z= 0.334
  Chirality :  0.045   0.173    907
  Planarity :  0.004   0.057   1026
  Dihedral  :  4.931  40.690    917
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.76 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 18.63 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.30), residues: 725
  helix:  1.91 (0.29), residues: 317
  sheet:  0.69 (0.42), residues: 147
  loop : -1.16 (0.33), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 114 
 HIS   0.002   0.001   HIS A 195 
 PHE   0.020   0.002   PHE B  47 
 TYR   0.016   0.002   TYR A 414 
 ARG   0.011   0.001   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04758 (  312)
  hydrogen bonds       : angle       4.23076 (  873)
  SS BOND              : bond        0.00348 (    1)
  SS BOND              : angle       0.73229 (    2)
  covalent geometry    : bond        0.00528 ( 6116)
  covalent geometry    : angle       0.61959 ( 8302)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6914 (ttt-90)
REVERT: C    3 GLN cc_start: 0.8443 (mp10) cc_final: 0.8176 (mp10)
REVERT: A  348 ARG cc_start: 0.8254 (mtm110) cc_final: 0.7911 (ttp80)
REVERT: A  372 MET cc_start: 0.8103 (mtp) cc_final: 0.7799 (mtt)
  outliers start: 22
  outliers final: 13
  residues processed: 95
  average time/residue: 1.1130
  time to fit residues: 111.3354
Evaluate side-chains
  92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   66 ARG
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   60 TYR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  552 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
C  73 ASN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

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 = 0.097731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.085792 restraints weight = 12614.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.97
r_work: 0.3154 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.4635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6117  Z= 0.180
  Angle     :  0.595   7.777   8304  Z= 0.319
  Chirality :  0.043   0.165    907
  Planarity :  0.004   0.052   1026
  Dihedral  :  4.891  42.872    917
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.21 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.43 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.30), residues: 725
  helix:  1.97 (0.29), residues: 317
  sheet:  0.58 (0.41), residues: 153
  loop : -1.11 (0.34), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 246 
 HIS   0.001   0.001   HIS A 195 
 PHE   0.017   0.001   PHE B  47 
 TYR   0.016   0.001   TYR A  46 
 ARG   0.010   0.001   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04438 (  312)
  hydrogen bonds       : angle       4.21430 (  873)
  SS BOND              : bond        0.00318 (    1)
  SS BOND              : angle       0.54899 (    2)
  covalent geometry    : bond        0.00411 ( 6116)
  covalent geometry    : angle       0.59523 ( 8302)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: B   30 LYS cc_start: 0.8698 (mptt) cc_final: 0.8498 (mmtt)
REVERT: B   66 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6853 (ttt-90)
REVERT: C    3 GLN cc_start: 0.8471 (mp10) cc_final: 0.8214 (mp10)
REVERT: A  242 MET cc_start: 0.9034 (tpp) cc_final: 0.8815 (tpp)
REVERT: A  348 ARG cc_start: 0.8216 (mtm110) cc_final: 0.7863 (ttp80)
REVERT: A  372 MET cc_start: 0.8065 (mtp) cc_final: 0.7814 (mtt)
  outliers start: 20
  outliers final: 12
  residues processed: 89
  average time/residue: 1.1099
  time to fit residues: 104.0519
Evaluate side-chains
  89 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   66 ARG
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  552 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
C  73 ASN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.097585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.085727 restraints weight = 12571.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.95
r_work: 0.3158 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.4723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6117  Z= 0.170
  Angle     :  0.592   7.772   8304  Z= 0.317
  Chirality :  0.043   0.167    907
  Planarity :  0.004   0.049   1026
  Dihedral  :  4.943  49.001    917
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.34 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.59 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.30), residues: 725
  helix:  1.96 (0.29), residues: 317
  sheet:  0.63 (0.42), residues: 151
  loop : -1.14 (0.34), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 246 
 HIS   0.001   0.001   HIS A 195 
 PHE   0.020   0.002   PHE A 447 
 TYR   0.016   0.001   TYR A 414 
 ARG   0.010   0.001   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04353 (  312)
  hydrogen bonds       : angle       4.18994 (  873)
  SS BOND              : bond        0.00300 (    1)
  SS BOND              : angle       0.63090 (    2)
  covalent geometry    : bond        0.00388 ( 6116)
  covalent geometry    : angle       0.59165 ( 8302)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
REVERT: B   30 LYS cc_start: 0.8690 (mptt) cc_final: 0.8473 (mmtt)
REVERT: B   66 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6895 (ttt-90)
REVERT: C    3 GLN cc_start: 0.8463 (mp10) cc_final: 0.8207 (mp10)
REVERT: A  348 ARG cc_start: 0.8213 (mtm110) cc_final: 0.7846 (ttp80)
REVERT: A  372 MET cc_start: 0.8041 (mtp) cc_final: 0.7759 (mtt)
  outliers start: 16
  outliers final: 14
  residues processed: 89
  average time/residue: 1.1717
  time to fit residues: 109.5361
Evaluate side-chains
  94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   66 ARG
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   60 TYR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  552 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0470
   chunk 1 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.1480

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
C  73 ASN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.097932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.086173 restraints weight = 12740.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.96
r_work: 0.3164 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.4732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6117  Z= 0.158
  Angle     :  0.606  12.368   8304  Z= 0.320
  Chirality :  0.042   0.168    907
  Planarity :  0.004   0.048   1026
  Dihedral  :  4.993  50.242    917
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.21 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.90 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.30), residues: 725
  helix:  1.99 (0.29), residues: 317
  sheet:  0.55 (0.41), residues: 153
  loop : -1.10 (0.34), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 246 
 HIS   0.001   0.001   HIS A 195 
 PHE   0.018   0.001   PHE A 447 
 TYR   0.017   0.001   TYR A 430 
 ARG   0.010   0.001   ARG C  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04237 (  312)
  hydrogen bonds       : angle       4.17357 (  873)
  SS BOND              : bond        0.00332 (    1)
  SS BOND              : angle       0.59283 (    2)
  covalent geometry    : bond        0.00362 ( 6116)
  covalent geometry    : angle       0.60555 ( 8302)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4730.07 seconds
wall clock time: 84 minutes 10.97 seconds (5050.97 seconds total)