Starting phenix.real_space_refine
on Wed Sep 17 10:23:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sp7_25367/09_2025/7sp7_25367.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sp7_25367/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sp7_25367/09_2025/7sp7_25367.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sp7_25367/09_2025/7sp7_25367.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sp7_25367/09_2025/7sp7_25367.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sp7_25367/09_2025/7sp7_25367.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.43, per 1000 atoms: 0.40
  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: 0.55
  Conformation dependent library (CDL) restraints added in 540.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.21
  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: 1.01

  Time building geometry restraints manager: 0.74 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:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.750
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.630
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (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
 ARG   0.002   0.000   ARG C  39 
 TYR   0.009   0.001   TYR A 430 
 PHE   0.007   0.001   PHE A 249 
 TRP   0.003   0.000   TRP A 502 
 HIS   0.001   0.000   HIS A 360 

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

*********************** 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  : 0.229 
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: 0.0796
  time to fit residues: 11.5846
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  : 0.265 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0870
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.3758

-------------------------------------------------------------------------------
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 = 0.3993 r_free = 0.3993 target = 0.157416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.127295 restraints weight = 20035.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 3.89
r_work: 0.3473 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.1414

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= 0.101
  Angle     :  0.444   7.865   8419  Z= 0.236
  Chirality :  0.041   0.213    911
  Planarity :  0.003   0.034   1034
  Dihedral  :  9.660 140.305    980
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  6.50 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.61 (0.32), residues: 732
  helix:  2.84 (0.29), residues: 319
  sheet:  1.94 (0.42), residues: 155
  loop :  0.16 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 256 
 TYR   0.019   0.001   TYR A 492 
 PHE   0.009   0.001   PHE B  47 
 TRP   0.022   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 6203)
  covalent geometry    : angle       0.44417 ( 8415)
  SS BOND              : bond        0.00282 (    2)
  SS BOND              : angle       0.72703 (    4)
  hydrogen bonds       : bond        0.03447 (  310)
  hydrogen bonds       : angle       3.93872 (  931)

*********************** 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
  90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  372 MET cc_start: 0.7744 (mmt) cc_final: 0.7387 (mmt)
REVERT: B   52 SER cc_start: 0.8929 (m) cc_final: 0.8593 (t)
REVERT: B   72 ASP cc_start: 0.6997 (t70) cc_final: 0.6614 (t70)
REVERT: B   86 LYS cc_start: 0.7212 (ptpp) cc_final: 0.6871 (ptpp)
  outliers start: 2
  outliers final: 1
  residues processed: 89
  average time/residue: 0.0762
  time to fit residues: 9.2808
Evaluate side-chains
  80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 7 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0770
   chunk 36 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0980
   chunk 35 optimal weight:    0.0980
   chunk 47 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.2738

-------------------------------------------------------------------------------
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 = 0.3958 r_free = 0.3958 target = 0.154499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.126768 restraints weight = 12839.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 3.07
r_work: 0.3485 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6205  Z= 0.089
  Angle     :  0.415   5.516   8419  Z= 0.222
  Chirality :  0.040   0.215    911
  Planarity :  0.003   0.035   1034
  Dihedral  :  8.967 116.259    980
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.92 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.32), residues: 732
  helix:  2.89 (0.29), residues: 320
  sheet:  1.76 (0.42), residues: 157
  loop :  0.15 (0.38), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  19 
 TYR   0.016   0.001   TYR A 492 
 PHE   0.007   0.001   PHE B  47 
 TRP   0.016   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00186 ( 6203)
  covalent geometry    : angle       0.41498 ( 8415)
  SS BOND              : bond        0.00296 (    2)
  SS BOND              : angle       0.74354 (    4)
  hydrogen bonds       : bond        0.03174 (  310)
  hydrogen bonds       : angle       3.61023 (  931)

*********************** 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
  93 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  372 MET cc_start: 0.7649 (mmt) cc_final: 0.7340 (mmt)
REVERT: B   52 SER cc_start: 0.8926 (m) cc_final: 0.8585 (t)
REVERT: B   72 ASP cc_start: 0.7084 (t70) cc_final: 0.6735 (t70)
REVERT: B   86 LYS cc_start: 0.7320 (ptpp) cc_final: 0.6958 (ptpp)
  outliers start: 5
  outliers final: 2
  residues processed: 90
  average time/residue: 0.0637
  time to fit residues: 8.2943
Evaluate side-chains
  85 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 SER
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 23 optimal weight:    0.0770
   chunk 45 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0060
   overall best weight:    0.4354

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.146765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.116358 restraints weight = 19803.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 3.84
r_work: 0.3325 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3355
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3355
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6205  Z= 0.103
  Angle     :  0.445   8.275   8419  Z= 0.237
  Chirality :  0.041   0.225    911
  Planarity :  0.003   0.039   1034
  Dihedral  :  8.757  90.514    980
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.08 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.34 (0.31), residues: 732
  helix:  2.80 (0.29), residues: 321
  sheet:  1.60 (0.42), residues: 150
  loop : -0.09 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  19 
 TYR   0.016   0.001   TYR A 492 
 PHE   0.011   0.001   PHE B  47 
 TRP   0.021   0.001   TRP A 351 
 HIS   0.001   0.000   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 6203)
  covalent geometry    : angle       0.44508 ( 8415)
  SS BOND              : bond        0.00222 (    2)
  SS BOND              : angle       0.83656 (    4)
  hydrogen bonds       : bond        0.03446 (  310)
  hydrogen bonds       : angle       3.44250 (  931)

*********************** 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
  91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  372 MET cc_start: 0.7863 (mmt) cc_final: 0.7589 (mmt)
REVERT: A  391 LYS cc_start: 0.7088 (mptt) cc_final: 0.6703 (mptt)
REVERT: B   52 SER cc_start: 0.9036 (m) cc_final: 0.8733 (t)
  outliers start: 8
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0818
  time to fit residues: 9.7025
Evaluate side-chains
  86 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   38 ARG
Chi-restraints excluded: chain B residue   68 THR
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 16 optimal weight:    0.0870
   chunk 64 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 35 optimal weight:    0.2980
   chunk 57 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.143631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.114151 restraints weight = 16957.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 3.52
r_work: 0.3305 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3330
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3331
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.3015

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= 0.106
  Angle     :  0.433   5.725   8419  Z= 0.233
  Chirality :  0.041   0.201    911
  Planarity :  0.003   0.039   1034
  Dihedral  :  8.657  88.686    980
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.14 %
    Favored  : 88.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.31), residues: 732
  helix:  2.73 (0.29), residues: 320
  sheet:  1.53 (0.41), residues: 149
  loop : -0.28 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  19 
 TYR   0.014   0.001   TYR A 492 
 PHE   0.010   0.001   PHE B  47 
 TRP   0.018   0.001   TRP A 351 
 HIS   0.001   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6203)
  covalent geometry    : angle       0.43285 ( 8415)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       0.72288 (    4)
  hydrogen bonds       : bond        0.03582 (  310)
  hydrogen bonds       : angle       3.45823 (  931)

*********************** 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
  84 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A  372 MET cc_start: 0.7735 (mmt) cc_final: 0.7461 (mmt)
REVERT: B   52 SER cc_start: 0.9018 (m) cc_final: 0.8762 (t)
  outliers start: 7
  outliers final: 7
  residues processed: 81
  average time/residue: 0.0863
  time to fit residues: 9.3484
Evaluate side-chains
  79 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 SER
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   76 ASN
Chi-restraints excluded: chain B residue   90 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 56 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0670
   chunk 21 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.9320

-------------------------------------------------------------------------------
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 = 0.3754 r_free = 0.3754 target = 0.136570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.108802 restraints weight = 13437.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 3.04
r_work: 0.3246 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    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 = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6205  Z= 0.156
  Angle     :  0.499   6.430   8419  Z= 0.268
  Chirality :  0.043   0.220    911
  Planarity :  0.003   0.034   1034
  Dihedral  :  8.253  85.073    980
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.62 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.31), residues: 732
  helix:  2.44 (0.29), residues: 325
  sheet:  1.12 (0.40), residues: 160
  loop : -0.45 (0.37), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  19 
 TYR   0.015   0.001   TYR A 492 
 PHE   0.016   0.001   PHE B  47 
 TRP   0.023   0.001   TRP A 351 
 HIS   0.002   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6203)
  covalent geometry    : angle       0.49884 ( 8415)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       0.91234 (    4)
  hydrogen bonds       : bond        0.04470 (  310)
  hydrogen bonds       : angle       3.69053 (  931)

*********************** 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
  82 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  372 MET cc_start: 0.7833 (mmt) cc_final: 0.7511 (mmt)
REVERT: B   52 SER cc_start: 0.9099 (m) cc_final: 0.8831 (t)
  outliers start: 9
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0892
  time to fit residues: 9.2175
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  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 SER
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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 3 optimal weight:    0.4980
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3765 r_free = 0.3765 target = 0.137708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.108259 restraints weight = 19261.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 3.66
r_work: 0.3223 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6205  Z= 0.118
  Angle     :  0.441   5.542   8419  Z= 0.239
  Chirality :  0.041   0.192    911
  Planarity :  0.003   0.036   1034
  Dihedral  :  7.982  86.722    980
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.73 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.31), residues: 732
  helix:  2.49 (0.29), residues: 325
  sheet:  1.26 (0.41), residues: 149
  loop : -0.41 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  75 
 TYR   0.014   0.001   TYR A 492 
 PHE   0.011   0.001   PHE B  47 
 TRP   0.023   0.001   TRP A 351 
 HIS   0.001   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6203)
  covalent geometry    : angle       0.44053 ( 8415)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       0.71338 (    4)
  hydrogen bonds       : bond        0.03957 (  310)
  hydrogen bonds       : angle       3.57521 (  931)

*********************** 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: 9
    poor density    : 67
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B   52 SER cc_start: 0.9108 (m) cc_final: 0.8841 (t)
REVERT: B   64 LYS cc_start: 0.6480 (mmmt) cc_final: 0.6232 (mmtt)
  outliers start: 9
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0817
  time to fit residues: 8.2387
Evaluate side-chains
  75 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 SER
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   68 THR
Chi-restraints excluded: chain B residue   76 ASN
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0770
   chunk 12 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0170
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.4976

-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.138727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.109156 restraints weight = 20866.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 3.80
r_work: 0.3230 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6205  Z= 0.102
  Angle     :  0.421   5.672   8419  Z= 0.228
  Chirality :  0.040   0.180    911
  Planarity :  0.003   0.038   1034
  Dihedral  :  7.631  89.866    980
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.89 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.31), residues: 732
  helix:  2.54 (0.29), residues: 325
  sheet:  1.23 (0.41), residues: 149
  loop : -0.39 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  75 
 TYR   0.013   0.001   TYR A 492 
 PHE   0.010   0.001   PHE B  47 
 TRP   0.018   0.001   TRP A 351 
 HIS   0.001   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 6203)
  covalent geometry    : angle       0.42065 ( 8415)
  SS BOND              : bond        0.00244 (    2)
  SS BOND              : angle       0.67898 (    4)
  hydrogen bonds       : bond        0.03702 (  310)
  hydrogen bonds       : angle       3.50248 (  931)

*********************** 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
  76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  301 ASP cc_start: 0.6440 (m-30) cc_final: 0.6098 (m-30)
REVERT: B   52 SER cc_start: 0.9080 (m) cc_final: 0.8852 (t)
  outliers start: 10
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0753
  time to fit residues: 7.7163
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  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  289 THR
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 25 optimal weight:    0.1980
   chunk 48 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 43 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.137154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.109860 restraints weight = 13732.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 3.06
r_work: 0.3257 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3280
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3280
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.4009

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= 0.114
  Angle     :  0.434   6.059   8419  Z= 0.235
  Chirality :  0.041   0.174    911
  Planarity :  0.003   0.038   1034
  Dihedral  :  7.601  89.226    980
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.73 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.31), residues: 732
  helix:  2.60 (0.29), residues: 319
  sheet:  1.19 (0.41), residues: 149
  loop : -0.36 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  71 
 TYR   0.013   0.001   TYR A 492 
 PHE   0.011   0.001   PHE B  47 
 TRP   0.017   0.001   TRP A 351 
 HIS   0.001   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6203)
  covalent geometry    : angle       0.43344 ( 8415)
  SS BOND              : bond        0.00199 (    2)
  SS BOND              : angle       0.71377 (    4)
  hydrogen bonds       : bond        0.03900 (  310)
  hydrogen bonds       : angle       3.51478 (  931)

*********************** 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: 11
    poor density    : 65
  time to evaluate  : 0.233 
Fit side-chains
REVERT: B   52 SER cc_start: 0.9076 (m) cc_final: 0.8833 (t)
  outliers start: 11
  outliers final: 11
  residues processed: 75
  average time/residue: 0.0818
  time to fit residues: 8.2708
Evaluate side-chains
  75 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  289 THR
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0670
   chunk 48 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.3764 r_free = 0.3764 target = 0.137738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.107899 restraints weight = 23452.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 3.98
r_work: 0.3207 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    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 = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6205  Z= 0.105
  Angle     :  0.428   6.254   8419  Z= 0.231
  Chirality :  0.040   0.167    911
  Planarity :  0.003   0.038   1034
  Dihedral  :  7.430  87.299    980
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.73 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.31), residues: 732
  helix:  2.62 (0.29), residues: 319
  sheet:  1.18 (0.41), residues: 149
  loop : -0.31 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  71 
 TYR   0.013   0.001   TYR A 492 
 PHE   0.010   0.001   PHE B  47 
 TRP   0.028   0.001   TRP A 351 
 HIS   0.001   0.001   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6203)
  covalent geometry    : angle       0.42812 ( 8415)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       0.67186 (    4)
  hydrogen bonds       : bond        0.03779 (  310)
  hydrogen bonds       : angle       3.49874 (  931)

********************** 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
  78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.231 
Fit side-chains
REVERT: B   52 SER cc_start: 0.9090 (m) cc_final: 0.8874 (t)
  outliers start: 11
  outliers final: 11
  residues processed: 77
  average time/residue: 0.0771
  time to fit residues: 8.1589
Evaluate side-chains
  76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  289 THR
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0030
   chunk 44 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0770
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   chunk 9 optimal weight:    0.0470
   chunk 64 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.3246

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.139556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.111218 restraints weight = 17160.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 3.44
r_work: 0.3264 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    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 = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6205  Z= 0.088
  Angle     :  0.404   6.283   8419  Z= 0.219
  Chirality :  0.040   0.165    911
  Planarity :  0.003   0.039   1034
  Dihedral  :  7.074  82.652    980
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 3.99
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.31), residues: 732
  helix:  2.72 (0.29), residues: 320
  sheet:  1.23 (0.41), residues: 149
  loop : -0.30 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  71 
 TYR   0.018   0.001   TYR C 106 
 PHE   0.007   0.001   PHE A  49 
 TRP   0.023   0.001   TRP A 351 
 HIS   0.001   0.000   HIS A 552 

Details of bonding type rmsd
  covalent geometry    : bond        0.00186 ( 6203)
  covalent geometry    : angle       0.40378 ( 8415)
  SS BOND              : bond        0.00265 (    2)
  SS BOND              : angle       0.61403 (    4)
  hydrogen bonds       : bond        0.03480 (  310)
  hydrogen bonds       : angle       3.43005 (  931)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1784.61 seconds
wall clock time: 31 minutes 13.33 seconds (1873.33 seconds total)