Starting phenix.real_space_refine
on Fri Jun  6 18:41:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sp7_25367/06_2025/7sp7_25367.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sp7_25367/06_2025/7sp7_25367.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sp7_25367/06_2025/7sp7_25367.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sp7_25367/06_2025/7sp7_25367.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sp7_25367/06_2025/7sp7_25367.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sp7_25367/06_2025/7sp7_25367.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.039
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 1820 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: 6
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P       3      5.49       5
     S      35      5.16       5
     C    3914      2.51       5
     N     991      2.21       5
     O    1107      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6052
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4064
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 497, 4053
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 13, 'TRANS': 483}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 497, 4053
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 13, 'TRANS': 483}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4152
    Chain: "B"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 950
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
    Chain: "C"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 925
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 113
          Unusual residues: {' MN': 2, '3PE': 1, 'UDP': 1, 'Y01': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 303 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 303 " occ=0.50
  Time building chain proxies: 6.12, per 1000 atoms: 1.01
  Number of scatterers: 6052
  At special positions: 0
  Unit cell: (71.28, 73.44, 154.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      2     24.99
     S      35     16.00
     P       3     15.00
     O    1107      8.00
     N     991      7.00
     C    3914      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    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: 1.77
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1372

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 9 sheets defined
      46.7% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 74
      removed outlier: 3.683A  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: 3.968A  pdb=" N   ALA A 131 " --> pdb=" O   ASP A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 160
      removed outlier: 4.044A  pdb=" N   THR A 159 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 189
      removed outlier: 3.510A  pdb=" N   TYR A 182 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 221
      Proline residue:  A 217  - end of helix
      removed outlier: 3.502A  pdb=" N   CYS A 220 " --> pdb=" O   TYR A 216 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP A 221 " --> pdb=" O   PRO A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 262
      removed outlier: 3.634A  pdb=" N   TRP A 246 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ARG A 256 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
      removed outlier: 4.979A  pdb=" N   GLY A 257 " --> pdb=" O   ASN A 253 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   TRP A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 289
      removed outlier: 5.337A  pdb=" N   ASP A 285 " --> pdb=" O   ASN A 281 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 300 through 312
      removed outlier: 3.982A  pdb=" N   LEU A 305 " --> pdb=" O   ASP A 301 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ARG A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 358
      removed outlier: 4.542A  pdb=" N   TRP A 351 " --> pdb=" O   CYS A 347 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   TYR A 352 " --> pdb=" O   ARG A 348 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   TRP A 358 " --> pdb=" O   LEU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 361
      No H-bonds generated for 'chain 'A' and resid 359 through 361'
    Processing helix  chain 'A' and resid 364 through 392
    Processing helix  chain 'A' and resid 393 through 420
    Processing helix  chain 'A' and resid 421 through 428
      removed outlier: 3.811A  pdb=" N   ALA A 424 " --> pdb=" O   ASN A 421 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE A 425 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL A 428 " --> pdb=" O   PHE A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 448
      removed outlier: 3.778A  pdb=" N   VAL A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ILE A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      Proline residue:  A 440  - end of helix
    Processing helix  chain 'A' and resid 470 through 497
      removed outlier: 6.382A  pdb=" N   ILE A 478 " --> pdb=" O   LYS A 474 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   THR A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 535
    Processing helix  chain 'A' and resid 539 through 551
      removed outlier: 3.538A  pdb=" N   GLU A 544 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 90
      removed outlier: 3.554A  pdb=" N   THR B  90 " --> pdb=" O   PRO B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 111
    Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143
      removed outlier: 3.773A  pdb=" N   ILE A 168 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   VAL A  84 " --> pdb=" O   ARG A 115 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   ILE A 117 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   VAL A  86 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   VAL A 119 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ILE A  88 " --> pdb=" O   VAL A 119 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ALA A  85 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   ILE A 200 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   ILE A  87 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLY A 273 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   LEU A 272 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY A 229 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   LYS A 225 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   ILE A 224 " --> pdb=" O   ILE A 316 " (cutoff:3.500A)
      removed outlier: 10.546A  pdb=" N   TYR A 318 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 10.695A  pdb=" N   ALA A 226 " --> pdb=" O   TYR A 318 " (cutoff:3.500A)
      removed outlier: 10.192A  pdb=" N   ALA A 228 " --> pdb=" O   PRO A 320 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ALA A 322 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501
      removed outlier: 6.459A  pdb=" N   PHE A 500 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 13
      removed outlier: 6.621A  pdb=" N   VAL B  12 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59
      removed outlier: 5.814A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA B  97 " --> pdb=" O   TYR B 113 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   TYR B 113 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59
      removed outlier: 5.814A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.795A  pdb=" N   ALA C  21 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   MET C  82 " --> pdb=" O   LEU C  18 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU C  18 " --> pdb=" O   MET C  82 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.795A  pdb=" N   ALA C  21 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 59
      removed outlier: 5.877A  pdb=" N   PHE C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ARG C  38 " --> pdb=" O   PHE C  47 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU C  34 " --> pdb=" O   SER C  51 " (cutoff:3.500A)

    330 hydrogen bonds defined for protein.
    931 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: 1.90

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 935
        1.28 -     1.41: 1717
        1.41 -     1.55: 3459
        1.55 -     1.68: 38
        1.68 -     1.81: 54
  Bond restraints: 6203
  Sorted by residual:
  bond pdb=" C3' UDP A 603 "
       pdb=" C2' UDP A 603 "
    ideal  model  delta    sigma   weight residual
    1.530  1.300  0.230 1.30e-02 5.92e+03 3.14e+02
  bond pdb=" C5  UDP A 603 "
       pdb=" C6  UDP A 603 "
    ideal  model  delta    sigma   weight residual
    1.343  1.511 -0.168 1.60e-02 3.91e+03 1.11e+02
  bond pdb=" C5' UDP A 603 "
       pdb=" C4' UDP A 603 "
    ideal  model  delta    sigma   weight residual
    1.508  1.397  0.111 1.10e-02 8.26e+03 1.01e+02
  bond pdb=" C2  UDP A 603 "
       pdb=" N3  UDP A 603 "
    ideal  model  delta    sigma   weight residual
    1.375  1.517 -0.142 1.70e-02 3.46e+03 7.00e+01
  bond pdb=" O3A UDP A 603 "
       pdb=" PB  UDP A 603 "
    ideal  model  delta    sigma   weight residual
    1.584  1.659 -0.075 1.00e-02 1.00e+04 5.67e+01
  ... (remaining 6198 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.91: 8307
        2.91 -     5.83: 88
        5.83 -     8.74: 14
        8.74 -    11.65: 3
       11.65 -    14.56: 3
  Bond angle restraints: 8415
  Sorted by residual:
  angle pdb=" C2  UDP A 603 "
        pdb=" N3  UDP A 603 "
        pdb=" C4  UDP A 603 "
      ideal   model   delta    sigma   weight residual
     126.93  120.20    6.73 1.00e+00 1.00e+00 4.54e+01
  angle pdb=" O2B UDP A 603 "
        pdb=" PB  UDP A 603 "
        pdb=" O3A UDP A 603 "
      ideal   model   delta    sigma   weight residual
     102.95  109.61   -6.66 1.00e+00 1.00e+00 4.43e+01
  angle pdb=" O1B UDP A 603 "
        pdb=" PB  UDP A 603 "
        pdb=" O3A UDP A 603 "
      ideal   model   delta    sigma   weight residual
     102.95  109.42   -6.47 1.00e+00 1.00e+00 4.19e+01
  angle pdb=" O5' UDP A 603 "
        pdb=" PA  UDP A 603 "
        pdb=" O3A UDP A 603 "
      ideal   model   delta    sigma   weight residual
     104.35  109.91   -5.56 1.00e+00 1.00e+00 3.09e+01
  angle pdb=" N1  UDP A 603 "
        pdb=" C2  UDP A 603 "
        pdb=" N3  UDP A 603 "
      ideal   model   delta    sigma   weight residual
     114.79  120.18   -5.39 1.00e+00 1.00e+00 2.91e+01
  ... (remaining 8410 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.01: 3602
       34.01 -    68.02: 72
       68.02 -   102.03: 11
      102.03 -   136.04: 0
      136.04 -   170.05: 1
  Dihedral angle restraints: 3686
    sinusoidal: 1529
      harmonic: 2157
  Sorted by residual:
  dihedral pdb=" O21 3PE A 601 "
           pdb=" C2  3PE A 601 "
           pdb=" C3  3PE A 601 "
           pdb=" O31 3PE A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.47 -129.48 -170.05     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.45   38.55     1      1.00e+01 1.00e-02 2.09e+01
  dihedral pdb=" CB  LYS A 314 "
           pdb=" CG  LYS A 314 "
           pdb=" CD  LYS A 314 "
           pdb=" CE  LYS A 314 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.86  -56.86     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 3683 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 841
       0.080 -    0.161: 62
       0.161 -    0.241: 3
       0.241 -    0.322: 2
       0.322 -    0.402: 3
  Chirality restraints: 911
  Sorted by residual:
  chirality pdb=" CBG Y01 A 602 "
            pdb=" CAQ Y01 A 602 "
            pdb=" CBD Y01 A 602 "
            pdb=" CBI Y01 A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.73    0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CBE Y01 A 602 "
            pdb=" CAP Y01 A 602 "
            pdb=" CBB Y01 A 602 "
            pdb=" CBI Y01 A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.92   -0.36 2.00e-01 2.50e+01 3.18e+00
  chirality pdb=" CBI Y01 A 602 "
            pdb=" CAU Y01 A 602 "
            pdb=" CBE Y01 A 602 "
            pdb=" CBG Y01 A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94    2.61    0.32 2.00e-01 2.50e+01 2.63e+00
  ... (remaining 908 not shown)

  Planarity restraints: 1034
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 270 "   -0.023 5.00e-02 4.00e+02   3.48e-02 1.93e+00
        pdb=" N   PRO A 271 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 319 "   -0.015 5.00e-02 4.00e+02   2.31e-02 8.52e-01
        pdb=" N   PRO A 320 "    0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A 320 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 320 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 251 "   -0.005 2.00e-02 2.50e+03   9.08e-03 8.24e-01
        pdb=" C   ALA A 251 "    0.016 2.00e-02 2.50e+03
        pdb=" O   ALA A 251 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   PHE A 252 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1031 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 653
        2.75 -     3.29: 5636
        3.29 -     3.83: 10081
        3.83 -     4.36: 11184
        4.36 -     4.90: 20097
  Nonbonded interactions: 47651
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  72 "
            pdb=" OG1 THR B  74 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O3' UDP A 603 "
            pdb=" O2' UDP A 603 "
     model   vdw
     2.367 2.432
  nonbonded pdb=" OE1 GLN A 186 "
            pdb=" NZ  LYS A 284 "
     model   vdw
     2.391 3.120
  nonbonded pdb=" O   TRP A 234 "
            pdb=" OG1 THR A 539 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" OG  SER C  17 "
            pdb=" O   MET C  82 "
     model   vdw
     2.401 3.040
  ... (remaining 47646 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=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:             1.160
  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:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.230
  Find NCS groups from input model:        0.070
  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:             0.010
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
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      :  0.008   0.230   6205  Z= 0.481
  Angle     :  0.680  14.565   8419  Z= 0.331
  Chirality :  0.047   0.402    911
  Planarity :  0.002   0.035   1034
  Dihedral  : 14.829 170.050   2308
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.32), residues: 732
  helix:  2.79 (0.29), residues: 317
  sheet:  1.89 (0.44), residues: 142
  loop :  0.20 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 502 
 HIS   0.001   0.000   HIS A 360 
 PHE   0.007   0.001   PHE A 249 
 TYR   0.009   0.001   TYR A 430 
 ARG   0.002   0.000   ARG C  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17645 (  310)
  hydrogen bonds       : angle       5.85320 (  931)
  SS BOND              : bond        0.00129 (    2)
  SS BOND              : angle       0.38054 (    4)
  covalent geometry    : bond        0.00753 ( 6203)
  covalent geometry    : angle       0.68061 ( 8415)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.592 
Fit side-chains
REVERT: A  372 MET cc_start: 0.7350 (mmt) cc_final: 0.7042 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1682
  time to fit residues: 24.5310
Evaluate side-chains
  81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 54 optimal weight:    0.0030
   chunk 30 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
A 307 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.152326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122609 restraints weight = 18177.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 3.68
r_work: 0.3420 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3445
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3445
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6205  Z= 0.122
  Angle     :  0.471   7.865   8419  Z= 0.250
  Chirality :  0.042   0.237    911
  Planarity :  0.003   0.034   1034
  Dihedral  :  9.742 140.611    980
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  6.50 %
    Favored  : 92.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.32), residues: 732
  helix:  2.76 (0.29), residues: 319
  sheet:  1.74 (0.42), residues: 157
  loop :  0.14 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 358 
 HIS   0.001   0.001   HIS A 552 
 PHE   0.014   0.001   PHE B  47 
 TYR   0.020   0.001   TYR A 492 
 ARG   0.003   0.000   ARG A 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03751 (  310)
  hydrogen bonds       : angle       3.92478 (  931)
  SS BOND              : bond        0.00240 (    2)
  SS BOND              : angle       0.85804 (    4)
  covalent geometry    : bond        0.00276 ( 6203)
  covalent geometry    : angle       0.47028 ( 8415)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A  372 MET cc_start: 0.7774 (mmt) cc_final: 0.7372 (mmt)
REVERT: B   72 ASP cc_start: 0.7197 (t70) cc_final: 0.6948 (t70)
REVERT: B   86 LYS cc_start: 0.7120 (ptpp) cc_final: 0.6879 (ptpp)
  outliers start: 4
  outliers final: 2
  residues processed: 90
  average time/residue: 0.1828
  time to fit residues: 21.6953
Evaluate side-chains
  82 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0870
   chunk 1 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 69 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.5556

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
A 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.145324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.116177 restraints weight = 15621.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 3.41
r_work: 0.3338 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6205  Z= 0.112
  Angle     :  0.446   4.845   8419  Z= 0.241
  Chirality :  0.041   0.219    911
  Planarity :  0.003   0.039   1034
  Dihedral  :  9.270 116.923    980
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  8.24 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.31), residues: 732
  helix:  2.68 (0.29), residues: 321
  sheet:  1.67 (0.43), residues: 150
  loop : -0.12 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 351 
 HIS   0.002   0.001   HIS A 552 
 PHE   0.011   0.001   PHE B  47 
 TYR   0.018   0.001   TYR A 492 
 ARG   0.011   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03798 (  310)
  hydrogen bonds       : angle       3.62728 (  931)
  SS BOND              : bond        0.00190 (    2)
  SS BOND              : angle       0.98206 (    4)
  covalent geometry    : bond        0.00250 ( 6203)
  covalent geometry    : angle       0.44607 ( 8415)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A  372 MET cc_start: 0.7766 (mmt) cc_final: 0.7438 (mmt)
REVERT: C   75 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8158 (mtm-85)
REVERT: C   82 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6341 (ptp)
  outliers start: 6
  outliers final: 3
  residues processed: 78
  average time/residue: 0.1782
  time to fit residues: 18.7673
Evaluate side-chains
  75 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ARG
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0170
   chunk 19 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7622

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.137669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.107694 restraints weight = 20058.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 3.78
r_work: 0.3208 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6205  Z= 0.136
  Angle     :  0.483   5.515   8419  Z= 0.262
  Chirality :  0.042   0.223    911
  Planarity :  0.004   0.041   1034
  Dihedral  :  9.453 108.400    980
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  8.87 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.90 (0.31), residues: 732
  helix:  2.45 (0.29), residues: 325
  sheet:  1.25 (0.40), residues: 161
  loop : -0.37 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 351 
 HIS   0.002   0.001   HIS A 552 
 PHE   0.017   0.001   PHE B  47 
 TYR   0.016   0.001   TYR A 492 
 ARG   0.007   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04242 (  310)
  hydrogen bonds       : angle       3.62274 (  931)
  SS BOND              : bond        0.00167 (    2)
  SS BOND              : angle       0.83013 (    4)
  covalent geometry    : bond        0.00316 ( 6203)
  covalent geometry    : angle       0.48280 ( 8415)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.608 
Fit side-chains
REVERT: A  372 MET cc_start: 0.7835 (mmt) cc_final: 0.7484 (mmt)
  outliers start: 12
  outliers final: 11
  residues processed: 78
  average time/residue: 0.1813
  time to fit residues: 19.2690
Evaluate side-chains
  80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 ASP
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   38 ARG
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   76 ASN
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 68 optimal weight:    0.2980
   chunk 55 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 69 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0050
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.4994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.140026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.114228 restraints weight = 9632.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.57
r_work: 0.3328 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6205  Z= 0.104
  Angle     :  0.432   4.931   8419  Z= 0.235
  Chirality :  0.040   0.195    911
  Planarity :  0.003   0.037   1034
  Dihedral  :  9.213  91.375    980
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.62 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.94 (0.31), residues: 732
  helix:  2.54 (0.29), residues: 325
  sheet:  1.20 (0.40), residues: 160
  loop : -0.40 (0.37), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 351 
 HIS   0.001   0.001   HIS A 552 
 PHE   0.009   0.001   PHE A 385 
 TYR   0.014   0.001   TYR A 492 
 ARG   0.007   0.000   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03724 (  310)
  hydrogen bonds       : angle       3.50866 (  931)
  SS BOND              : bond        0.00253 (    2)
  SS BOND              : angle       0.68247 (    4)
  covalent geometry    : bond        0.00232 ( 6203)
  covalent geometry    : angle       0.43160 ( 8415)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  372 MET cc_start: 0.7606 (mmt) cc_final: 0.7264 (mmt)
  outliers start: 12
  outliers final: 10
  residues processed: 76
  average time/residue: 0.1764
  time to fit residues: 18.3031
Evaluate side-chains
  76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   38 ARG
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    0.0060
   chunk 40 optimal weight:    0.4980
   chunk 62 optimal weight:    0.0870
   chunk 6 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.3774

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.141171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.114695 restraints weight = 11033.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.75
r_work: 0.3332 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3358
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3358
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6205  Z= 0.092
  Angle     :  0.409   5.009   8419  Z= 0.222
  Chirality :  0.040   0.176    911
  Planarity :  0.003   0.039   1034
  Dihedral  :  8.582  89.446    980
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.41 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.31), residues: 732
  helix:  2.70 (0.29), residues: 320
  sheet:  1.15 (0.40), residues: 160
  loop : -0.36 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 351 
 HIS   0.001   0.000   HIS A 552 
 PHE   0.007   0.001   PHE B  47 
 TYR   0.013   0.001   TYR A 492 
 ARG   0.006   0.000   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  310)
  hydrogen bonds       : angle       3.43041 (  931)
  SS BOND              : bond        0.00273 (    2)
  SS BOND              : angle       0.59812 (    4)
  covalent geometry    : bond        0.00200 ( 6203)
  covalent geometry    : angle       0.40917 ( 8415)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A  304 ARG cc_start: 0.7725 (tpt170) cc_final: 0.7437 (tpt170)
REVERT: A  333 MET cc_start: 0.8230 (mmm) cc_final: 0.8010 (mmt)
REVERT: C   18 LEU cc_start: 0.7369 (pp) cc_final: 0.7095 (mp)
  outliers start: 9
  outliers final: 9
  residues processed: 75
  average time/residue: 0.1754
  time to fit residues: 18.0735
Evaluate side-chains
  72 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   38 ARG
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0980
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.136824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108249 restraints weight = 16928.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 3.41
r_work: 0.3223 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6205  Z= 0.126
  Angle     :  0.448   5.594   8419  Z= 0.244
  Chirality :  0.041   0.159    911
  Planarity :  0.003   0.037   1034
  Dihedral  :  8.049  89.718    980
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.94 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.83 (0.31), residues: 732
  helix:  2.46 (0.29), residues: 325
  sheet:  1.07 (0.40), residues: 161
  loop : -0.41 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 351 
 HIS   0.001   0.001   HIS A 360 
 PHE   0.011   0.001   PHE B  47 
 TYR   0.014   0.001   TYR A 492 
 ARG   0.005   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04062 (  310)
  hydrogen bonds       : angle       3.51864 (  931)
  SS BOND              : bond        0.00232 (    2)
  SS BOND              : angle       0.73255 (    4)
  covalent geometry    : bond        0.00293 ( 6203)
  covalent geometry    : angle       0.44812 ( 8415)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.649 
Fit side-chains
REVERT: C   18 LEU cc_start: 0.7508 (pp) cc_final: 0.7112 (mp)
  outliers start: 12
  outliers final: 12
  residues processed: 75
  average time/residue: 0.1639
  time to fit residues: 16.9331
Evaluate side-chains
  73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   38 ARG
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.134820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.105858 restraints weight = 20269.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 3.68
r_work: 0.3192 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6205  Z= 0.140
  Angle     :  0.467   5.847   8419  Z= 0.253
  Chirality :  0.041   0.156    911
  Planarity :  0.003   0.038   1034
  Dihedral  :  7.981  87.038    980
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.89 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.69 (0.31), residues: 732
  helix:  2.37 (0.28), residues: 326
  sheet:  0.92 (0.40), residues: 160
  loop : -0.44 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 351 
 HIS   0.002   0.001   HIS A 552 
 PHE   0.012   0.001   PHE B  47 
 TYR   0.020   0.001   TYR C 106 
 ARG   0.004   0.001   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  310)
  hydrogen bonds       : angle       3.57932 (  931)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       0.81121 (    4)
  covalent geometry    : bond        0.00330 ( 6203)
  covalent geometry    : angle       0.46704 ( 8415)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.616 
Fit side-chains
REVERT: B   64 LYS cc_start: 0.6832 (mmmt) cc_final: 0.6612 (mmtt)
  outliers start: 11
  outliers final: 11
  residues processed: 75
  average time/residue: 0.1581
  time to fit residues: 16.5743
Evaluate side-chains
  73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   38 ARG
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 53 optimal weight:    0.0370
   chunk 31 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0000
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 66 optimal weight:    0.1980
   chunk 2 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.3262

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.138951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.110745 restraints weight = 17350.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 3.43
r_work: 0.3253 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6205  Z= 0.092
  Angle     :  0.412   5.957   8419  Z= 0.223
  Chirality :  0.040   0.139    911
  Planarity :  0.003   0.040   1034
  Dihedral  :  7.425  87.880    980
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.04 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.95 (0.31), residues: 732
  helix:  2.66 (0.29), residues: 320
  sheet:  1.00 (0.40), residues: 160
  loop : -0.33 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 351 
 HIS   0.001   0.000   HIS A 360 
 PHE   0.007   0.001   PHE A  49 
 TYR   0.016   0.001   TYR C 106 
 ARG   0.004   0.000   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03537 (  310)
  hydrogen bonds       : angle       3.44295 (  931)
  SS BOND              : bond        0.00236 (    2)
  SS BOND              : angle       0.62129 (    4)
  covalent geometry    : bond        0.00195 ( 6203)
  covalent geometry    : angle       0.41199 ( 8415)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.609 
Fit side-chains
REVERT: C   18 LEU cc_start: 0.7469 (pp) cc_final: 0.7122 (mp)
  outliers start: 9
  outliers final: 9
  residues processed: 75
  average time/residue: 0.1764
  time to fit residues: 17.8285
Evaluate side-chains
  73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   38 ARG
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 16 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.106653 restraints weight = 20077.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 3.67
r_work: 0.3198 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6205  Z= 0.130
  Angle     :  0.450   6.011   8419  Z= 0.245
  Chirality :  0.041   0.143    911
  Planarity :  0.003   0.038   1034
  Dihedral  :  7.556  87.734    980
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.20 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.31), residues: 732
  helix:  2.50 (0.29), residues: 319
  sheet:  1.15 (0.41), residues: 150
  loop : -0.44 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 351 
 HIS   0.001   0.001   HIS A 552 
 PHE   0.013   0.001   PHE B  47 
 TYR   0.016   0.001   TYR C 106 
 ARG   0.004   0.000   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04068 (  310)
  hydrogen bonds       : angle       3.55758 (  931)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       0.78931 (    4)
  covalent geometry    : bond        0.00306 ( 6203)
  covalent geometry    : angle       0.44970 ( 8415)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.635 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1716
  time to fit residues: 17.5536
Evaluate side-chains
  72 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   38 ARG
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0770
   chunk 29 optimal weight:    0.1980
   chunk 7 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0980
   chunk 20 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.3138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.138412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.108842 restraints weight = 23909.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 4.00
r_work: 0.3220 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.4052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6205  Z= 0.091
  Angle     :  0.412   6.099   8419  Z= 0.224
  Chirality :  0.039   0.135    911
  Planarity :  0.003   0.040   1034
  Dihedral  :  7.175  83.724    980
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.68 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.92 (0.31), residues: 732
  helix:  2.67 (0.29), residues: 319
  sheet:  0.97 (0.40), residues: 160
  loop : -0.36 (0.37), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 351 
 HIS   0.001   0.000   HIS A 552 
 PHE   0.008   0.001   PHE A  49 
 TYR   0.016   0.001   TYR C 106 
 ARG   0.004   0.000   ARG C  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03559 (  310)
  hydrogen bonds       : angle       3.45513 (  931)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       0.59020 (    4)
  covalent geometry    : bond        0.00193 ( 6203)
  covalent geometry    : angle       0.41142 ( 8415)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3508.22 seconds
wall clock time: 61 minutes 10.27 seconds (3670.27 seconds total)