Starting phenix.real_space_refine
on Thu Jul  2 07:55:16 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7sp9_25369/07_2026/7sp9_25369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sp9_25369/07_2026/7sp9_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sp9_25369/07_2026/7sp9_25369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sp9_25369/07_2026/7sp9_25369.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7sp9_25369/07_2026/7sp9_25369.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7sp9_25369/07_2026/7sp9_25369.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sp9_25369/07_2026/7sp9_25369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sp9_25369/07_2026/7sp9_25369.map"
  }
  resolution = 2.9
  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=  -0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.41, per 1000 atoms: 0.24
  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: 0.42
  Conformation dependent library (CDL) restraints added in 147.3 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: 0.17
  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: 0.90

  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 -     1.33: 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: 3264
       16.23 -    32.47: 201
       32.47 -    48.70: 46
       48.70 -    64.93: 9
       64.93 -    81.16: 5
  Dihedral angle restraints: 3525
    sinusoidal: 1379
      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 3522 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:             1.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.750
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
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  : 11.907  81.163   2156
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.005   0.000   ARG A  67 
 TYR   0.013   0.001   TYR A 414 
 PHE   0.019   0.001   PHE A 447 
 TRP   0.019   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 552 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.22 ( 6116)
  covalent geometry    : angle       0.56784 /  0.26 ( 8302)
  SS BOND              : bond        0.00293 /  0.15 (    1)
  SS BOND              : angle       0.15093 /  0.08 (    2)
  hydrogen bonds       : bond        0.18663 / 12.58 (  312)
  hydrogen bonds       : angle       6.48689 /  4.49 (  873)

*********************** 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  : 0.171 
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: 0.4079
  time to fit residues: 53.4636
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  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0570
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8702

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.111362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.098786 restraints weight = 12532.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.06
r_work: 0.3366 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6117  Z= 0.147
  Angle     :  0.552   7.214   8304  Z= 0.286
  Chirality :  0.042   0.129    907
  Planarity :  0.004   0.039   1026
  Dihedral  :  4.679  54.499    835
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.21 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.62 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 are not related in a simple way.
  whole:  1.44 (0.31), residues: 725
  helix:  2.13 (0.29), residues: 311
  sheet:  1.35 (0.43), residues: 149
  loop : -0.74 (0.35), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  39 
 TYR   0.013   0.001   TYR A 528 
 PHE   0.020   0.002   PHE A  49 
 TRP   0.012   0.001   TRP A 262 
 HIS   0.001   0.001   HIS A 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.15 ( 6116)
  covalent geometry    : angle       0.55173 /  0.29 ( 8302)
  SS BOND              : bond        0.00575 /  0.30 (    1)
  SS BOND              : angle       0.86010 /  0.46 (    2)
  hydrogen bonds       : bond        0.03901 /  2.59 (  312)
  hydrogen bonds       : angle       4.38643 /  3.07 (  873)

*********************** 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
  115 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.6982 (ttm-80) cc_final: 0.6691 (ttt-90)
REVERT: B   84 SER cc_start: 0.7990 (p) cc_final: 0.7745 (t)
REVERT: B   89 ASP cc_start: 0.7390 (m-30) cc_final: 0.7087 (m-30)
REVERT: C   28 ILE cc_start: 0.7278 (pt) cc_final: 0.6957 (pt)
REVERT: A  348 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7797 (ptp90)
REVERT: A  426 TYR cc_start: 0.8720 (m-10) cc_final: 0.8435 (m-10)
  outliers start: 15
  outliers final: 10
  residues processed: 106
  average time/residue: 0.4635
  time to fit residues: 52.0160
Evaluate side-chains
  89 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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 44 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 1 optimal weight:    9.9990
   overall best weight:    0.9782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.105776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.093043 restraints weight = 12535.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.07
r_work: 0.3248 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6117  Z= 0.142
  Angle     :  0.531   6.756   8304  Z= 0.277
  Chirality :  0.041   0.144    907
  Planarity :  0.003   0.027   1026
  Dihedral  :  4.558  57.910    835
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.93 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 13.06 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 are not related in a simple way.
  whole:  1.38 (0.31), residues: 725
  helix:  2.16 (0.29), residues: 312
  sheet:  1.03 (0.42), residues: 152
  loop : -0.69 (0.35), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  27 
 TYR   0.013   0.001   TYR A 383 
 PHE   0.013   0.001   PHE A  49 
 TRP   0.009   0.001   TRP A 262 
 HIS   0.002   0.001   HIS A 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 6116)
  covalent geometry    : angle       0.53085 /  0.28 ( 8302)
  SS BOND              : bond        0.00433 /  0.23 (    1)
  SS BOND              : angle       0.49079 /  0.26 (    2)
  hydrogen bonds       : bond        0.04147 /  2.73 (  312)
  hydrogen bonds       : angle       4.16518 /  2.96 (  873)

*********************** 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
  111 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.232 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.6994 (ttm-80) cc_final: 0.6639 (ttt-90)
REVERT: A  348 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7729 (ptp90)
REVERT: A  372 MET cc_start: 0.7864 (mtp) cc_final: 0.7620 (mtt)
REVERT: A  530 ILE cc_start: 0.8947 (tt) cc_final: 0.8695 (pt)
REVERT: A  547 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8332 (tp30)
  outliers start: 21
  outliers final: 15
  residues processed: 101
  average time/residue: 0.5166
  time to fit residues: 54.9516
Evaluate side-chains
  89 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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   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   80 LEU
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  255 GLU
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 9 optimal weight:    0.0570
   chunk 12 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0570
   chunk 16 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 23 optimal weight:   10.0000
   overall best weight:    0.8220

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 253 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.105030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.092623 restraints weight = 12375.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.98
r_work: 0.3254 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.3424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6117  Z= 0.123
  Angle     :  0.507   6.727   8304  Z= 0.267
  Chirality :  0.041   0.149    907
  Planarity :  0.003   0.037   1026
  Dihedral  :  4.489  58.746    835
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.21 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 15.61 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 are not related in a simple way.
  whole:  1.37 (0.31), residues: 725
  helix:  2.14 (0.29), residues: 312
  sheet:  1.00 (0.42), residues: 152
  loop : -0.69 (0.35), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  75 
 TYR   0.014   0.001   TYR A 430 
 PHE   0.013   0.001   PHE A  49 
 TRP   0.007   0.001   TRP A 262 
 HIS   0.001   0.001   HIS A 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 6116)
  covalent geometry    : angle       0.50719 /  0.27 ( 8302)
  SS BOND              : bond        0.00365 /  0.19 (    1)
  SS BOND              : angle       0.39478 /  0.21 (    2)
  hydrogen bonds       : bond        0.03780 /  2.49 (  312)
  hydrogen bonds       : angle       4.05200 /  2.88 (  873)

*********************** 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: 23
    poor density    : 90
  time to evaluate  : 0.245 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6605 (ttt-90)
REVERT: C    3 GLN cc_start: 0.8593 (mp10) cc_final: 0.8385 (mp10)
REVERT: A  253 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8256 (m-40)
REVERT: A  348 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7714 (ptp90)
REVERT: A  372 MET cc_start: 0.7900 (mtp) cc_final: 0.7630 (mtt)
REVERT: A  530 ILE cc_start: 0.8965 (tt) cc_final: 0.8591 (pt)
  outliers start: 23
  outliers final: 12
  residues processed: 101
  average time/residue: 0.4418
  time to fit residues: 46.9184
Evaluate side-chains
  93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   66 ARG
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  253 ASN
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  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 0 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.3184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.101889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.089695 restraints weight = 12437.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.95
r_work: 0.3205 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.3825

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= 0.168
  Angle     :  0.550   6.874   8304  Z= 0.295
  Chirality :  0.043   0.174    907
  Planarity :  0.004   0.032   1026
  Dihedral  :  4.673  57.878    835
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.93 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 16.24 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 are not related in a simple way.
  whole:  1.22 (0.31), residues: 725
  helix:  2.04 (0.29), residues: 312
  sheet:  0.93 (0.43), residues: 152
  loop : -0.80 (0.34), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  75 
 TYR   0.015   0.001   TYR A 430 
 PHE   0.022   0.002   PHE A 252 
 TRP   0.008   0.001   TRP A 262 
 HIS   0.001   0.001   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.17 ( 6116)
  covalent geometry    : angle       0.55047 /  0.30 ( 8302)
  SS BOND              : bond        0.00361 /  0.19 (    1)
  SS BOND              : angle       0.46763 /  0.25 (    2)
  hydrogen bonds       : bond        0.04223 /  2.77 (  312)
  hydrogen bonds       : angle       4.12826 /  2.93 (  873)

*********************** 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
  108 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.233 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6796 (ttt-90)
REVERT: B   72 ASP cc_start: 0.7494 (t0) cc_final: 0.7277 (t0)
REVERT: C    3 GLN cc_start: 0.8525 (mp10) cc_final: 0.8321 (mp10)
REVERT: C   25 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8399 (p)
REVERT: A  348 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7598 (ptp90)
REVERT: A  372 MET cc_start: 0.8005 (mtp) cc_final: 0.7725 (mtt)
  outliers start: 24
  outliers final: 17
  residues processed: 97
  average time/residue: 0.4804
  time to fit residues: 49.1634
Evaluate side-chains
  97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
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   78 VAL
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   25 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 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  266 GLN
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  552 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 18 optimal weight:    0.1980
   chunk 20 optimal weight:    0.3980
   chunk 11 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.102835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.090551 restraints weight = 12309.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.97
r_work: 0.3222 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6117  Z= 0.116
  Angle     :  0.511   7.182   8304  Z= 0.270
  Chirality :  0.041   0.155    907
  Planarity :  0.003   0.026   1026
  Dihedral  :  4.484  53.495    835
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.21 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.36 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 are not related in a simple way.
  whole:  1.26 (0.30), residues: 725
  helix:  2.11 (0.29), residues: 312
  sheet:  1.06 (0.43), residues: 145
  loop : -0.85 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  27 
 TYR   0.013   0.001   TYR A 414 
 PHE   0.015   0.001   PHE A 447 
 TRP   0.007   0.001   TRP A 262 
 HIS   0.001   0.001   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 ( 6116)
  covalent geometry    : angle       0.51139 /  0.27 ( 8302)
  SS BOND              : bond        0.00343 /  0.18 (    1)
  SS BOND              : angle       0.47163 /  0.25 (    2)
  hydrogen bonds       : bond        0.03727 /  2.45 (  312)
  hydrogen bonds       : angle       4.01762 /  2.85 (  873)

*********************** 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
  99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.240 
Fit side-chains
REVERT: C    3 GLN cc_start: 0.8501 (mp10) cc_final: 0.8277 (mp10)
REVERT: C   25 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8422 (p)
REVERT: A  242 MET cc_start: 0.9006 (tpp) cc_final: 0.8800 (tpp)
REVERT: A  348 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7621 (ttp80)
REVERT: A  372 MET cc_start: 0.7935 (mtp) cc_final: 0.7623 (mtt)
REVERT: A  530 ILE cc_start: 0.8973 (tt) cc_final: 0.8657 (pt)
  outliers start: 17
  outliers final: 11
  residues processed: 91
  average time/residue: 0.4857
  time to fit residues: 46.3264
Evaluate side-chains
  88 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   25 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   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  552 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0050
   chunk 57 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8798

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.101883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.089752 restraints weight = 12425.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.94
r_work: 0.3209 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6117  Z= 0.132
  Angle     :  0.530   7.500   8304  Z= 0.283
  Chirality :  0.041   0.158    907
  Planarity :  0.003   0.026   1026
  Dihedral  :  4.446  48.697    835
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.34 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 16.24 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 are not related in a simple way.
  whole:  1.24 (0.30), residues: 725
  helix:  2.09 (0.29), residues: 312
  sheet:  1.07 (0.43), residues: 145
  loop : -0.88 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  27 
 TYR   0.014   0.001   TYR A 414 
 PHE   0.012   0.001   PHE B  47 
 TRP   0.007   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 6116)
  covalent geometry    : angle       0.53001 /  0.28 ( 8302)
  SS BOND              : bond        0.00315 /  0.17 (    1)
  SS BOND              : angle       0.52422 /  0.28 (    2)
  hydrogen bonds       : bond        0.03887 /  2.53 (  312)
  hydrogen bonds       : angle       3.95428 /  2.81 (  873)

*********************** 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
  110 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.228 
Fit side-chains
REVERT: B   66 ARG cc_start: 0.6791 (ttt-90) cc_final: 0.6488 (ttt-90)
REVERT: C    3 GLN cc_start: 0.8500 (mp10) cc_final: 0.8267 (mp10)
REVERT: C   25 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8454 (p)
REVERT: A  348 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7639 (ptp90)
REVERT: A  372 MET cc_start: 0.7952 (mtp) cc_final: 0.7631 (mtt)
REVERT: A  530 ILE cc_start: 0.8973 (tt) cc_final: 0.8609 (pt)
  outliers start: 26
  outliers final: 16
  residues processed: 98
  average time/residue: 0.5188
  time to fit residues: 53.3224
Evaluate side-chains
  96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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   69 ILE
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   25 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  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  552 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.095815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.083774 restraints weight = 12585.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.93
r_work: 0.3101 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.4783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   6117  Z= 0.295
  Angle     :  0.688   7.382   8304  Z= 0.372
  Chirality :  0.048   0.198    907
  Planarity :  0.005   0.037   1026
  Dihedral  :  5.234  41.274    835
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.17 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 16.72 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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 are not related in a simple way.
  whole:  0.73 (0.30), residues: 725
  helix:  1.70 (0.28), residues: 317
  sheet:  0.44 (0.41), residues: 161
  loop : -1.07 (0.35), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  27 
 TYR   0.017   0.002   TYR A 430 
 PHE   0.023   0.002   PHE B  47 
 TRP   0.010   0.002   TRP A 262 
 HIS   0.003   0.001   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00681 /  0.30 ( 6116)
  covalent geometry    : angle       0.68751 /  0.37 ( 8302)
  SS BOND              : bond        0.00229 /  0.12 (    1)
  SS BOND              : angle       0.78292 /  0.41 (    2)
  hydrogen bonds       : bond        0.05496 /  3.58 (  312)
  hydrogen bonds       : angle       4.44926 /  3.16 (  873)

*********************** 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
  109 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.247 
Fit side-chains
REVERT: B   30 LYS cc_start: 0.8704 (mptt) cc_final: 0.8503 (mmtt)
REVERT: B   49 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8676 (m)
REVERT: B   66 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6670 (ttt-90)
REVERT: C   60 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.8223 (OUTLIER)
REVERT: C   75 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7957 (mtm-85)
REVERT: A  348 ARG cc_start: 0.8181 (mtm110) cc_final: 0.7818 (ttp80)
REVERT: A  372 MET cc_start: 0.8223 (mtp) cc_final: 0.7980 (mtt)
  outliers start: 25
  outliers final: 15
  residues processed: 96
  average time/residue: 0.4977
  time to fit residues: 50.2849
Evaluate side-chains
  92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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    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  255 GLU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  523 ILE
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 35 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.099396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.087309 restraints weight = 12492.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.96
r_work: 0.3172 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6117  Z= 0.132
  Angle     :  0.579   8.788   8304  Z= 0.306
  Chirality :  0.042   0.164    907
  Planarity :  0.003   0.031   1026
  Dihedral  :  4.694  37.141    835
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.34 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 19.75 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 are not related in a simple way.
  whole:  1.07 (0.31), residues: 725
  helix:  2.04 (0.29), residues: 317
  sheet:  0.88 (0.43), residues: 145
  loop : -1.08 (0.34), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  27 
 TYR   0.015   0.001   TYR A 414 
 PHE   0.016   0.001   PHE A 447 
 TRP   0.008   0.001   TRP A 262 
 HIS   0.001   0.001   HIS A 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 6116)
  covalent geometry    : angle       0.57891 /  0.31 ( 8302)
  SS BOND              : bond        0.00350 /  0.18 (    1)
  SS BOND              : angle       0.46628 /  0.26 (    2)
  hydrogen bonds       : bond        0.04043 /  2.62 (  312)
  hydrogen bonds       : angle       4.15579 /  2.94 (  873)

*********************** 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
  97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.218 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.6418 (t70) cc_final: 0.6136 (p0)
REVERT: C    3 GLN cc_start: 0.8591 (mp10) cc_final: 0.8362 (mp10)
REVERT: C   60 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.8151 (OUTLIER)
REVERT: A  348 ARG cc_start: 0.8144 (mtm110) cc_final: 0.7792 (ttp80)
REVERT: A  372 MET cc_start: 0.7998 (mtp) cc_final: 0.7730 (mtt)
REVERT: A  405 THR cc_start: 0.9009 (m) cc_final: 0.8795 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 89
  average time/residue: 0.4873
  time to fit residues: 45.5383
Evaluate side-chains
  86 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
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   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 A residue  552 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3466 r_free = 0.3466 target = 0.099410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.087457 restraints weight = 12424.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.93
r_work: 0.3170 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.4580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6117  Z= 0.138
  Angle     :  0.583   7.255   8304  Z= 0.311
  Chirality :  0.042   0.173    907
  Planarity :  0.004   0.037   1026
  Dihedral  :  4.518  37.916    835
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.07 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.11 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 are not related in a simple way.
  whole:  1.10 (0.30), residues: 725
  helix:  2.00 (0.29), residues: 317
  sheet:  1.11 (0.43), residues: 141
  loop : -1.09 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  75 
 TYR   0.017   0.001   TYR A  46 
 PHE   0.013   0.001   PHE B  47 
 TRP   0.007   0.001   TRP A 346 
 HIS   0.001   0.001   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.14 ( 6116)
  covalent geometry    : angle       0.58279 /  0.31 ( 8302)
  SS BOND              : bond        0.00404 /  0.21 (    1)
  SS BOND              : angle       0.58452 /  0.32 (    2)
  hydrogen bonds       : bond        0.04119 /  2.66 (  312)
  hydrogen bonds       : angle       4.10872 /  2.91 (  873)

********************** 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
  97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.225 
Fit side-chains
REVERT: B   61 ASP cc_start: 0.6437 (t70) cc_final: 0.6061 (p0)
REVERT: C    3 GLN cc_start: 0.8582 (mp10) cc_final: 0.8352 (mp10)
REVERT: C   60 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.8166 (OUTLIER)
REVERT: A  334 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.8209 (mmm-85)
REVERT: A  348 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7787 (ttp80)
REVERT: A  372 MET cc_start: 0.8054 (mtp) cc_final: 0.7763 (mtt)
  outliers start: 16
  outliers final: 10
  residues processed: 87
  average time/residue: 0.4869
  time to fit residues: 44.6024
Evaluate side-chains
  85 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
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   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   77 THR
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 30 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.099794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.087783 restraints weight = 12468.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.94
r_work: 0.3175 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.4560

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= 0.136
  Angle     :  0.588  12.335   8304  Z= 0.310
  Chirality :  0.043   0.332    907
  Planarity :  0.004   0.032   1026
  Dihedral  :  4.494  40.774    835
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.21 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 20.06 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.31), residues: 725
  helix:  2.03 (0.29), residues: 317
  sheet:  1.10 (0.42), residues: 141
  loop : -1.08 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  75 
 TYR   0.015   0.001   TYR A  46 
 PHE   0.013   0.001   PHE A  49 
 TRP   0.029   0.001   TRP A 346 
 HIS   0.001   0.001   HIS A 195 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 ( 6116)
  covalent geometry    : angle       0.58839 /  0.31 ( 8302)
  SS BOND              : bond        0.00344 /  0.18 (    1)
  SS BOND              : angle       0.52739 /  0.29 (    2)
  hydrogen bonds       : bond        0.04079 /  2.65 (  312)
  hydrogen bonds       : angle       4.06622 /  2.88 (  873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1905.62 seconds
wall clock time: 33 minutes 13.90 seconds (1993.90 seconds total)