Starting phenix.real_space_refine
on Wed Feb 12 18:13:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sp8_25368/02_2025/7sp8_25368.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sp8_25368/02_2025/7sp8_25368.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sp8_25368/02_2025/7sp8_25368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sp8_25368/02_2025/7sp8_25368.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sp8_25368/02_2025/7sp8_25368.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sp8_25368/02_2025/7sp8_25368.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.791
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    3935      2.51       5
     N     999      2.21       5
     O    1116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6090
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4088
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 500, 4077
          Classifications: {'peptide': 500}
          Link IDs: {'PTRANS': 13, 'TRANS': 486}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 500, 4077
          Classifications: {'peptide': 500}
          Link IDs: {'PTRANS': 13, 'TRANS': 486}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4176
    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: 127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 127
          Unusual residues: {' MN': 2, '3PE': 1, 'UD1': 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: 5.93, per 1000 atoms: 0.97
  Number of scatterers: 6090
  At special positions: 0
  Unit cell: (73.44, 72.36, 153.36, 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    1116      8.00
     N     999      7.00
     C    3935      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: 1.81
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1378

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 8 sheets defined
      47.3% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 74
      removed outlier: 3.648A  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: 3.655A  pdb=" N   ALA A 131 " --> pdb=" O   ASP A 127 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
      removed outlier: 3.509A  pdb=" N   SER A 152 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 190
    Processing helix  chain 'A' and resid 209 through 221
      Proline residue:  A 217  - end of helix
      removed outlier: 3.560A  pdb=" N   CYS A 220 " --> pdb=" O   TYR A 216 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ASP A 221 " --> pdb=" O   PRO A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 262
      removed outlier: 4.051A  pdb=" N   ARG A 256 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   GLY A 257 " --> pdb=" O   ASN A 253 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   TRP A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 289
      removed outlier: 5.221A  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 303 through 312
    Processing helix  chain 'A' and resid 331 through 357
      removed outlier: 4.281A  pdb=" N   TRP A 351 " --> pdb=" O   CYS A 347 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   TYR A 352 " --> pdb=" O   ARG A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 361
    Processing helix  chain 'A' and resid 364 through 392
    Processing helix  chain 'A' and resid 393 through 420
      removed outlier: 3.507A  pdb=" N   GLN A 397 " --> pdb=" O   ASP A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 428
      removed outlier: 3.707A  pdb=" N   ALA A 424 " --> pdb=" O   ASN A 421 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE A 425 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL A 428 " --> pdb=" O   PHE A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 449
      removed outlier: 4.031A  pdb=" N   VAL A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
      removed outlier: 4.421A  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 468 through 497
      removed outlier: 4.083A  pdb=" N   GLN A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE A 476 " --> pdb=" O   TRP A 472 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ILE A 478 " --> pdb=" O   LYS A 474 " (cutoff:3.500A)
      removed outlier: 5.082A  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: 3.750A  pdb=" N   LYS A 543 " --> pdb=" O   THR A 539 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   GLU A 544 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.522A  pdb=" N   THR B  31 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 90
    Processing helix  chain 'C' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143
      removed outlier: 3.656A  pdb=" N   ILE A 168 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   VAL A  84 " --> pdb=" O   ARG A 115 " (cutoff:3.500A)
      removed outlier: 8.517A  pdb=" N   ILE A 117 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   VAL A  86 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   VAL A 119 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ILE A  88 " --> pdb=" O   VAL A 119 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A  89 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   LEU A 272 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   LYS A 225 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   ILE A 224 " --> pdb=" O   ILE A 316 " (cutoff:3.500A)
      removed outlier: 10.639A  pdb=" N   TYR A 318 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 10.789A  pdb=" N   ALA A 226 " --> pdb=" O   TYR A 318 " (cutoff:3.500A)
      removed outlier: 10.388A  pdb=" N   ALA A 228 " --> pdb=" O   PRO A 320 " (cutoff:3.500A)
      removed outlier: 6.694A  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: 6.554A  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
      removed outlier: 3.630A  pdb=" N   SER B  21 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU B  18 " --> pdb=" O   MET B  82 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL B  20 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 13
      removed outlier: 6.292A  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: 5.877A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL B  92 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59
      removed outlier: 5.877A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL B  92 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.592A  pdb=" N   LEU C  18 " --> pdb=" O   MET C  82 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU C  20 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 59
      removed outlier: 6.050A  pdb=" N   PHE C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ARG C  38 " --> pdb=" O   PHE C  47 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ALA C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU C  34 " --> pdb=" O   SER C  51 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   TYR C  93 " --> pdb=" O   GLY C 119 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   GLY C 119 " --> pdb=" O   TYR C  93 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   CYS C  95 " --> pdb=" O   GLY C 117 " (cutoff:3.500A)

    337 hydrogen bonds defined for protein.
    945 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: 1.82

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 942
        1.31 -     1.43: 1856
        1.43 -     1.56: 3363
        1.56 -     1.69: 28
        1.69 -     1.81: 53
  Bond restraints: 6242
  Sorted by residual:
  bond pdb=" C2B UD1 A 601 "
       pdb=" C3B UD1 A 601 "
    ideal  model  delta    sigma   weight residual
    1.533  1.303  0.230 2.00e-02 2.50e+03 1.32e+02
  bond pdb=" C5  UD1 A 601 "
       pdb=" C6  UD1 A 601 "
    ideal  model  delta    sigma   weight residual
    1.342  1.484 -0.142 2.00e-02 2.50e+03 5.06e+01
  bond pdb=" C2  UD1 A 601 "
       pdb=" N3  UD1 A 601 "
    ideal  model  delta    sigma   weight residual
    1.371  1.501 -0.130 2.00e-02 2.50e+03 4.24e+01
  bond pdb=" CBD Y01 A 603 "
       pdb=" CBG Y01 A 603 "
    ideal  model  delta    sigma   weight residual
    1.520  1.644 -0.124 2.00e-02 2.50e+03 3.82e+01
  bond pdb=" C7' UD1 A 601 "
       pdb=" N2' UD1 A 601 "
    ideal  model  delta    sigma   weight residual
    1.347  1.465 -0.118 2.00e-02 2.50e+03 3.49e+01
  ... (remaining 6237 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.27: 8374
        3.27 -     6.55: 74
        6.55 -     9.82: 13
        9.82 -    13.10: 4
       13.10 -    16.37: 4
  Bond angle restraints: 8469
  Sorted by residual:
  angle pdb=" O1' UD1 A 601 "
        pdb=" PB  UD1 A 601 "
        pdb=" O3A UD1 A 601 "
      ideal   model   delta    sigma   weight residual
      92.88  109.25  -16.37 3.00e+00 1.11e-01 2.98e+01
  angle pdb=" O3A UD1 A 601 "
        pdb=" PA  UD1 A 601 "
        pdb=" O5B UD1 A 601 "
      ideal   model   delta    sigma   weight residual
      94.40  109.61  -15.21 3.00e+00 1.11e-01 2.57e+01
  angle pdb=" O12 3PE A 602 "
        pdb=" P   3PE A 602 "
        pdb=" O14 3PE A 602 "
      ideal   model   delta    sigma   weight residual
     123.79  109.19   14.60 3.00e+00 1.11e-01 2.37e+01
  angle pdb=" CAM Y01 A 603 "
        pdb=" CAY Y01 A 603 "
        pdb=" OAW Y01 A 603 "
      ideal   model   delta    sigma   weight residual
     111.19  124.36  -13.17 3.00e+00 1.11e-01 1.93e+01
  angle pdb=" CAI Y01 A 603 "
        pdb=" CAZ Y01 A 603 "
        pdb=" CAV Y01 A 603 "
      ideal   model   delta    sigma   weight residual
     120.03  131.68  -11.65 3.00e+00 1.11e-01 1.51e+01
  ... (remaining 8464 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.02: 3558
       28.02 -    56.04: 147
       56.04 -    84.06: 19
       84.06 -   112.08: 1
      112.08 -   140.10: 1
  Dihedral angle restraints: 3726
    sinusoidal: 1560
      harmonic: 2166
  Sorted by residual:
  dihedral pdb=" O21 3PE A 602 "
           pdb=" C2  3PE A 602 "
           pdb=" C3  3PE A 602 "
           pdb=" O31 3PE A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.47 -159.43 -140.10     1      3.00e+01 1.11e-03 1.88e+01
  dihedral pdb=" CA  GLU A 548 "
           pdb=" C   GLU A 548 "
           pdb=" N   ARG A 549 "
           pdb=" CA  ARG A 549 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.54   17.46     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  ASP C  59 "
           pdb=" CB  ASP C  59 "
           pdb=" CG  ASP C  59 "
           pdb=" OD1 ASP C  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.64   54.64     1      2.00e+01 2.50e-03 1.01e+01
  ... (remaining 3723 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 844
       0.079 -    0.158: 62
       0.158 -    0.237: 8
       0.237 -    0.316: 2
       0.316 -    0.395: 3
  Chirality restraints: 919
  Sorted by residual:
  chirality pdb=" CBG Y01 A 603 "
            pdb=" CAQ Y01 A 603 "
            pdb=" CBD Y01 A 603 "
            pdb=" CBI Y01 A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.73    0.40 2.00e-01 2.50e+01 3.90e+00
  chirality pdb=" CBE Y01 A 603 "
            pdb=" CAP Y01 A 603 "
            pdb=" CBB Y01 A 603 "
            pdb=" CBI Y01 A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.93   -0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" CBI Y01 A 603 "
            pdb=" CAU Y01 A 603 "
            pdb=" CBE Y01 A 603 "
            pdb=" CBG Y01 A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.94    2.61    0.33 2.00e-01 2.50e+01 2.71e+00
  ... (remaining 916 not shown)

  Planarity restraints: 1040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 544 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.84e+00
        pdb=" C   GLU A 544 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLU A 544 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A 545 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  86 "    0.021 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO B  87 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B  87 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B  87 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 545 "   -0.006 2.00e-02 2.50e+03   1.16e-02 1.34e+00
        pdb=" C   LEU A 545 "    0.020 2.00e-02 2.50e+03
        pdb=" O   LEU A 545 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ILE A 546 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1037 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 454
        2.74 -     3.28: 5804
        3.28 -     3.82: 10316
        3.82 -     4.36: 11542
        4.36 -     4.90: 20548
  Nonbonded interactions: 48664
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 203 "
            pdb="MN    MN A 605 "
     model   vdw
     2.204 2.320
  nonbonded pdb=" OE2 GLU A  93 "
            pdb="MN    MN A 604 "
     model   vdw
     2.247 2.320
  nonbonded pdb=" O   TRP A 234 "
            pdb=" OG1 THR A 539 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OE1 GLN A 506 "
            pdb=" OG1 THR B  56 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OD2 ASP B 104 "
            pdb=" OG1 THR B 107 "
     model   vdw
     2.321 3.040
  ... (remaining 48659 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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.760
  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:             0.000
  Load rotamer database and sin/cos tables:12.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
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   6242  Z= 0.499
  Angle     :  0.770  16.370   8469  Z= 0.303
  Chirality :  0.049   0.395    919
  Planarity :  0.003   0.031   1040
  Dihedral  : 14.940 140.099   2342
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.47 %
    Favored  : 99.37 %
  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:  2.53 (0.32), residues: 735
  helix:  2.59 (0.30), residues: 316
  sheet:  2.50 (0.42), residues: 161
  loop : -0.08 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.000   TRP A 346 
 HIS   0.001   0.000   HIS A 552 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.008   0.001   TYR A 414 
 ARG   0.001   0.000   ARG A 247 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.641 
Fit side-chains
REVERT: C   28 ILE cc_start: 0.7720 (mm) cc_final: 0.7186 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.9270
  time to fit residues: 139.0056
Evaluate side-chains
  109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 55 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
A 537 ASN
B  39 GLN
B  73 ASN
C  76 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.096092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.079420 restraints weight = 29568.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 3.24
r_work: 0.3018 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6242  Z= 0.175
  Angle     :  0.527   6.631   8469  Z= 0.271
  Chirality :  0.041   0.160    919
  Planarity :  0.003   0.025   1040
  Dihedral  :  9.444 105.813   1008
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  :  9.32 %
    Favored  : 87.05 %
  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:  2.36 (0.31), residues: 735
  helix:  2.69 (0.29), residues: 318
  sheet:  2.02 (0.41), residues: 154
  loop : -0.16 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 470 
 HIS   0.002   0.001   HIS A 174 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.013   0.001   TYR A 414 
 ARG   0.004   0.000   ARG B  38 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  544 GLU cc_start: 0.7665 (mp0) cc_final: 0.7465 (mp0)
REVERT: B    3 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7502 (mp-120)
REVERT: C   25 SER cc_start: 0.9152 (m) cc_final: 0.8809 (p)
  outliers start: 22
  outliers final: 8
  residues processed: 129
  average time/residue: 0.9448
  time to fit residues: 129.4221
Evaluate side-chains
  124 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain B residue    3 GLN
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   79 CYS
Chi-restraints excluded: chain C residue  111 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 67 optimal weight:    0.2980
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
A 338 GLN
A 339 GLN
B  73 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.090917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.073745 restraints weight = 31730.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 3.31
r_work: 0.2906 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2907
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2907
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6242  Z= 0.168
  Angle     :  0.506   8.928   8469  Z= 0.264
  Chirality :  0.042   0.146    919
  Planarity :  0.003   0.031   1040
  Dihedral  :  8.981  90.156   1008
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 12.64 %
    Favored  : 84.20 %
  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:  2.28 (0.31), residues: 735
  helix:  2.57 (0.29), residues: 320
  sheet:  1.94 (0.40), residues: 156
  loop : -0.14 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 360 
 PHE   0.015   0.001   PHE A  49 
 TYR   0.013   0.001   TYR A 414 
 ARG   0.005   0.000   ARG B  66 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.663 
Fit side-chains
REVERT: A  239 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8475 (tp)
REVERT: C   25 SER cc_start: 0.9156 (m) cc_final: 0.8893 (p)
REVERT: C   85 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8822 (mt)
  outliers start: 19
  outliers final: 9
  residues processed: 121
  average time/residue: 1.0049
  time to fit residues: 129.0167
Evaluate side-chains
  117 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  111 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 8 optimal weight:    0.0870
   chunk 57 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 62 optimal weight:    0.4980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
A 506 GLN
B  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.089138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.072677 restraints weight = 23986.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.88
r_work: 0.2890 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6242  Z= 0.159
  Angle     :  0.508   8.623   8469  Z= 0.262
  Chirality :  0.041   0.159    919
  Planarity :  0.003   0.036   1040
  Dihedral  :  8.822  77.523   1008
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 13.11 %
    Favored  : 82.46 %
  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:  2.22 (0.31), residues: 735
  helix:  2.52 (0.29), residues: 320
  sheet:  2.06 (0.40), residues: 159
  loop : -0.31 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.015   0.001   PHE A  49 
 TYR   0.016   0.001   TYR C 106 
 ARG   0.002   0.000   ARG B  66 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  239 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8375 (tp)
REVERT: C   11 LEU cc_start: 0.8009 (tm) cc_final: 0.7766 (tt)
REVERT: C   25 SER cc_start: 0.9172 (m) cc_final: 0.8895 (p)
REVERT: C   85 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8936 (mt)
  outliers start: 27
  outliers final: 11
  residues processed: 120
  average time/residue: 1.0064
  time to fit residues: 127.8785
Evaluate side-chains
  114 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 27 optimal weight:    8.9990
   chunk 51 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 331 ASN
B  73 ASN
C  83 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.087460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.070295 restraints weight = 36165.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 3.45
r_work: 0.2828 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6242  Z= 0.170
  Angle     :  0.515   7.277   8469  Z= 0.266
  Chirality :  0.042   0.215    919
  Planarity :  0.003   0.038   1040
  Dihedral  :  8.806  66.024   1008
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 14.69 %
    Favored  : 80.88 %
  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:  2.12 (0.30), residues: 735
  helix:  2.44 (0.29), residues: 320
  sheet:  2.05 (0.39), residues: 149
  loop : -0.29 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.018   0.001   TYR C 106 
 ARG   0.002   0.000   ARG A 106 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A  247 ARG cc_start: 0.8902 (tpp-160) cc_final: 0.8550 (tpm-80)
REVERT: C   85 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8793 (mt)
  outliers start: 26
  outliers final: 11
  residues processed: 115
  average time/residue: 1.0393
  time to fit residues: 126.2190
Evaluate side-chains
  113 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 72 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0060
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
B  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.087744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.070883 restraints weight = 29348.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 3.13
r_work: 0.2846 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2848
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2848 r_free = 0.2848    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2848
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.3500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6242  Z= 0.162
  Angle     :  0.522   7.439   8469  Z= 0.270
  Chirality :  0.042   0.181    919
  Planarity :  0.003   0.038   1040
  Dihedral  :  8.718  61.273   1008
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.43 %
    Favored  : 79.94 %
  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:  2.10 (0.30), residues: 735
  helix:  2.47 (0.29), residues: 320
  sheet:  1.94 (0.39), residues: 149
  loop : -0.33 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 360 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.019   0.001   TYR C 106 
 ARG   0.002   0.000   ARG B  38 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.668 
Fit side-chains
REVERT: B   72 ASP cc_start: 0.8456 (t0) cc_final: 0.8209 (t0)
REVERT: C   11 LEU cc_start: 0.8273 (tm) cc_final: 0.8023 (tt)
REVERT: C   85 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8852 (mt)
  outliers start: 21
  outliers final: 13
  residues processed: 112
  average time/residue: 1.0028
  time to fit residues: 118.9594
Evaluate side-chains
  115 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 71 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.085241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.068299 restraints weight = 31230.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 3.22
r_work: 0.2787 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.3833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6242  Z= 0.214
  Angle     :  0.553   8.223   8469  Z= 0.286
  Chirality :  0.043   0.178    919
  Planarity :  0.003   0.039   1040
  Dihedral  :  8.738  59.001   1008
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.37 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.90 %
    Favored  : 80.09 %
  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:  1.93 (0.30), residues: 735
  helix:  2.30 (0.29), residues: 322
  sheet:  1.63 (0.39), residues: 163
  loop : -0.34 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 472 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.016   0.001   TYR C 106 
 ARG   0.002   0.000   ARG A 106 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.674 
Fit side-chains
REVERT: B   18 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8435 (mm)
REVERT: B   72 ASP cc_start: 0.8545 (t0) cc_final: 0.8258 (t0)
REVERT: C   25 SER cc_start: 0.9197 (m) cc_final: 0.8821 (p)
REVERT: C   43 LYS cc_start: 0.8832 (ptpt) cc_final: 0.8580 (mtmm)
  outliers start: 17
  outliers final: 11
  residues processed: 112
  average time/residue: 1.0287
  time to fit residues: 121.9302
Evaluate side-chains
  113 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  120 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
B  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.084635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.068161 restraints weight = 22557.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 2.77
r_work: 0.2802 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.4010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6242  Z= 0.219
  Angle     :  0.556   7.644   8469  Z= 0.290
  Chirality :  0.043   0.168    919
  Planarity :  0.003   0.039   1040
  Dihedral  :  8.646  57.714   1008
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.50 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.01 %
    Favored  : 79.30 %
  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:  1.93 (0.30), residues: 735
  helix:  2.34 (0.29), residues: 319
  sheet:  1.64 (0.39), residues: 163
  loop : -0.36 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.015   0.001   PHE A  49 
 TYR   0.019   0.001   TYR C 106 
 ARG   0.002   0.000   ARG A 106 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.731 
Fit side-chains
REVERT: A   51 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8718 (mt)
REVERT: B    3 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7858 (mp10)
REVERT: B   18 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8491 (mm)
REVERT: B   44 GLU cc_start: 0.8690 (pm20) cc_final: 0.8354 (pm20)
REVERT: B   72 ASP cc_start: 0.8337 (t0) cc_final: 0.8019 (t0)
REVERT: C   43 LYS cc_start: 0.8834 (ptpt) cc_final: 0.8588 (mtmm)
REVERT: C   89 ASP cc_start: 0.8289 (m-30) cc_final: 0.8025 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 107
  average time/residue: 1.0112
  time to fit residues: 114.3845
Evaluate side-chains
  109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  111 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.7558

-------------------------------------------------------------------------------
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 = 0.3274 r_free = 0.3274 target = 0.085389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.068243 restraints weight = 32441.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 3.29
r_work: 0.2788 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6242  Z= 0.187
  Angle     :  0.557   8.488   8469  Z= 0.286
  Chirality :  0.042   0.158    919
  Planarity :  0.003   0.038   1040
  Dihedral  :  8.452  59.619   1008
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.33 %
    Favored  : 79.30 %
  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:  1.89 (0.30), residues: 735
  helix:  2.35 (0.29), residues: 319
  sheet:  1.55 (0.39), residues: 165
  loop : -0.40 (0.36), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.018   0.001   TYR C 106 
 ARG   0.003   0.000   ARG C  45 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A   51 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8637 (mt)
REVERT: A  299 TYR cc_start: 0.7057 (p90) cc_final: 0.6624 (m-80)
REVERT: B    3 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7860 (mp10)
REVERT: B   18 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8495 (mm)
REVERT: B   72 ASP cc_start: 0.8346 (t0) cc_final: 0.8041 (t0)
REVERT: C   43 LYS cc_start: 0.8838 (ptpt) cc_final: 0.8595 (mtmm)
  outliers start: 13
  outliers final: 9
  residues processed: 105
  average time/residue: 1.0015
  time to fit residues: 112.0207
Evaluate side-chains
  108 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  111 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0870
   chunk 53 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.9962

-------------------------------------------------------------------------------
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 = 0.3260 r_free = 0.3260 target = 0.084609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.068105 restraints weight = 23710.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 2.82
r_work: 0.2798 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2798
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2798 r_free = 0.2798    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2798 r_free = 0.2798    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2798
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.4123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6242  Z= 0.217
  Angle     :  0.570   8.047   8469  Z= 0.295
  Chirality :  0.043   0.160    919
  Planarity :  0.003   0.040   1040
  Dihedral  :  8.350  57.038   1008
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.37 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.80 %
    Favored  : 79.15 %
  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:  1.85 (0.31), residues: 735
  helix:  2.32 (0.29), residues: 319
  sheet:  1.47 (0.39), residues: 165
  loop : -0.39 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 472 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.015   0.001   PHE A  49 
 TYR   0.016   0.001   TYR C 106 
 ARG   0.002   0.000   ARG A 106 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A   51 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8735 (mt)
REVERT: A  247 ARG cc_start: 0.8992 (tpp-160) cc_final: 0.8657 (tpm-80)
REVERT: B    3 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7891 (mp10)
REVERT: B   18 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8531 (mm)
REVERT: B   72 ASP cc_start: 0.8310 (t0) cc_final: 0.8017 (t0)
REVERT: C   25 SER cc_start: 0.9112 (m) cc_final: 0.8787 (p)
  outliers start: 11
  outliers final: 8
  residues processed: 103
  average time/residue: 0.9968
  time to fit residues: 108.9568
Evaluate side-chains
  107 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  111 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0370
   chunk 13 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.085690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.069693 restraints weight = 20187.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.60
r_work: 0.2833 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6242  Z= 0.177
  Angle     :  0.559   8.454   8469  Z= 0.286
  Chirality :  0.042   0.151    919
  Planarity :  0.003   0.039   1040
  Dihedral  :  8.166  56.652   1008
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.12 %
    Favored  : 78.83 %
  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:  1.89 (0.31), residues: 735
  helix:  2.36 (0.29), residues: 319
  sheet:  1.55 (0.39), residues: 162
  loop : -0.42 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.015   0.001   PHE A  49 
 TYR   0.019   0.001   TYR C 106 
 ARG   0.002   0.000   ARG C  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4637.43 seconds
wall clock time: 82 minutes 41.00 seconds (4961.00 seconds total)