Starting phenix.real_space_refine
on Wed Mar 12 18:49:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sp8_25368/03_2025/7sp8_25368.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sp8_25368/03_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_25368/03_2025/7sp8_25368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sp8_25368/03_2025/7sp8_25368.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sp8_25368/03_2025/7sp8_25368.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sp8_25368/03_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-5624/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: 6.22, per 1000 atoms: 1.02
  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: 1.74
  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: 0.69
  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: 1.73

  Time building geometry restraints manager: 2.02 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:             0.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.030
  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:12.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.290
-------------------------------------------------------------------------------
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  : 0.839 
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: 0.9138
  time to fit residues: 136.8778
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  : 0.634 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3488 r_free = 0.3488 target = 0.097695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.081228 restraints weight = 29835.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 3.26
r_work: 0.3052 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6242  Z= 0.161
  Angle     :  0.522   6.758   8469  Z= 0.267
  Chirality :  0.041   0.160    919
  Planarity :  0.003   0.024   1040
  Dihedral  :  9.427 105.626   1008
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  :  9.16 %
    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:  2.44 (0.31), residues: 735
  helix:  2.71 (0.29), residues: 318
  sheet:  2.11 (0.41), residues: 158
  loop : -0.12 (0.36), residues: 259

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   0.012   0.001   TYR A  46 
 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
  141 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.632 
Fit side-chains
REVERT: A  239 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8342 (tp)
REVERT: B    3 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7459 (mp-120)
REVERT: C   25 SER cc_start: 0.9138 (m) cc_final: 0.8802 (p)
  outliers start: 23
  outliers final: 6
  residues processed: 127
  average time/residue: 1.0117
  time to fit residues: 136.3870
Evaluate side-chains
  124 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain B residue    3 GLN
Chi-restraints excluded: chain B residue   92 VAL
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:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0980
   chunk 23 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    0.2980
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.093831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.076975 restraints weight = 32244.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 3.38
r_work: 0.2966 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6242  Z= 0.145
  Angle     :  0.493   8.082   8469  Z= 0.258
  Chirality :  0.041   0.141    919
  Planarity :  0.003   0.030   1040
  Dihedral  :  8.897  91.800   1008
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 12.01 %
    Favored  : 84.99 %
  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:  2.66 (0.29), residues: 319
  sheet:  1.95 (0.40), residues: 158
  loop : -0.12 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 470 
 HIS   0.002   0.001   HIS A 360 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.011   0.001   TYR A 414 
 ARG   0.006   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
  133 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.642 
Fit side-chains
REVERT: A  239 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8415 (tp)
REVERT: A  422 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9111 (mp)
REVERT: C   25 SER cc_start: 0.9146 (m) cc_final: 0.8888 (p)
  outliers start: 18
  outliers final: 7
  residues processed: 120
  average time/residue: 1.0105
  time to fit residues: 128.2592
Evaluate side-chains
  117 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
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  422 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   68 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 8 optimal weight:    0.0040
   chunk 57 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 506 GLN
B  73 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.089779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.073184 restraints weight = 23967.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 2.90
r_work: 0.2908 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2911
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2911 r_free = 0.2911    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2911 r_free = 0.2911    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2911
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6242  Z= 0.165
  Angle     :  0.506   8.154   8469  Z= 0.264
  Chirality :  0.041   0.147    919
  Planarity :  0.003   0.033   1040
  Dihedral  :  8.732  78.153   1008
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 12.80 %
    Favored  : 82.62 %
  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:  2.19 (0.31), residues: 735
  helix:  2.54 (0.29), residues: 320
  sheet:  1.73 (0.40), residues: 158
  loop : -0.14 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.015   0.001   TYR C 106 
 ARG   0.004   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
  141 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A  239 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8387 (tp)
REVERT: A  544 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7477 (pm20)
  outliers start: 28
  outliers final: 10
  residues processed: 127
  average time/residue: 1.1321
  time to fit residues: 153.6266
Evaluate side-chains
  115 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
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  384 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  544 GLU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0570
   chunk 56 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.6298

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.088962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.071701 restraints weight = 36248.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 3.48
r_work: 0.2858 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6242  Z= 0.160
  Angle     :  0.499   6.991   8469  Z= 0.261
  Chirality :  0.041   0.205    919
  Planarity :  0.003   0.036   1040
  Dihedral  :  8.669  66.350   1008
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.96 %
    Favored  : 80.57 %
  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:  2.16 (0.30), residues: 735
  helix:  2.48 (0.29), residues: 320
  sheet:  2.04 (0.39), residues: 149
  loop : -0.27 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 472 
 HIS   0.002   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 B  66 

*********************** 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
  127 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A  239 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8409 (tp)
REVERT: A  544 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7516 (pm20)
REVERT: B   72 ASP cc_start: 0.8844 (t0) cc_final: 0.8600 (t0)
  outliers start: 21
  outliers final: 12
  residues processed: 114
  average time/residue: 1.2667
  time to fit residues: 152.3481
Evaluate side-chains
  116 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
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 A residue  544 GLU
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
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:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0470
   chunk 72 optimal weight:    4.9990
   chunk 69 optimal weight:    8.9990
   chunk 65 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0060
   chunk 14 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.4294

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.089461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.072574 restraints weight = 29565.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 3.20
r_work: 0.2886 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   6242  Z= 0.148
  Angle     :  0.517   8.453   8469  Z= 0.264
  Chirality :  0.041   0.146    919
  Planarity :  0.003   0.036   1040
  Dihedral  :  8.606  59.903   1008
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 16.59 %
    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:  2.13 (0.30), residues: 735
  helix:  2.49 (0.29), residues: 320
  sheet:  1.95 (0.39), residues: 159
  loop : -0.39 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 360 
 PHE   0.013   0.001   PHE A  49 
 TYR   0.018   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: 20
    poor density    : 104
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A  239 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8364 (tp)
REVERT: B   18 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8325 (mm)
  outliers start: 20
  outliers final: 11
  residues processed: 112
  average time/residue: 0.9671
  time to fit residues: 114.7591
Evaluate side-chains
  115 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
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  433 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain C residue   43 LYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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
B 119 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.086909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.069704 restraints weight = 30972.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 3.26
r_work: 0.2822 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6242  Z= 0.197
  Angle     :  0.532   7.206   8469  Z= 0.278
  Chirality :  0.042   0.141    919
  Planarity :  0.003   0.039   1040
  Dihedral  :  8.595  57.592   1008
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.50 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.90 %
    Favored  : 79.46 %
  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:  2.02 (0.31), residues: 735
  helix:  2.35 (0.29), residues: 322
  sheet:  1.83 (0.39), residues: 161
  loop : -0.35 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.021   0.001   TYR C 106 
 ARG   0.002   0.000   ARG C  45 

*********************** 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
  125 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.733 
Fit side-chains
REVERT: B   18 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8398 (mm)
REVERT: B   67 PHE cc_start: 0.9233 (m-10) cc_final: 0.8980 (m-10)
  outliers start: 21
  outliers final: 11
  residues processed: 111
  average time/residue: 1.0798
  time to fit residues: 126.8836
Evaluate side-chains
  112 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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    7 SER
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  111 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  73 ASN
B 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.086894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.070582 restraints weight = 22450.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.76
r_work: 0.2851 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2853
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2853 r_free = 0.2853    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 = 0.2853 r_free = 0.2853    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6242  Z= 0.181
  Angle     :  0.544   8.635   8469  Z= 0.279
  Chirality :  0.042   0.138    919
  Planarity :  0.003   0.038   1040
  Dihedral  :  8.493  59.356   1008
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.37 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.33 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.30), residues: 735
  helix:  2.36 (0.28), residues: 322
  sheet:  1.80 (0.39), residues: 161
  loop : -0.35 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.020   0.001   TYR C 106 
 ARG   0.002   0.000   ARG B  38 

*********************** 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
  120 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.623 
Fit side-chains
REVERT: A  299 TYR cc_start: 0.6971 (p90) cc_final: 0.6546 (m-80)
REVERT: B   18 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8376 (mm)
REVERT: B   72 ASP cc_start: 0.8633 (t0) cc_final: 0.8395 (t0)
REVERT: C   43 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8511 (mtmm)
  outliers start: 18
  outliers final: 12
  residues processed: 110
  average time/residue: 1.0050
  time to fit residues: 116.9141
Evaluate side-chains
  113 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
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    7 SER
Chi-restraints excluded: chain C residue   32 ASP
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:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B  73 ASN
B 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.086386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.069490 restraints weight = 33232.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 3.33
r_work: 0.2826 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.3864

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= 0.216
  Angle     :  0.573   8.071   8469  Z= 0.297
  Chirality :  0.042   0.143    919
  Planarity :  0.003   0.039   1040
  Dihedral  :  8.386  57.469   1008
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.37 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.80 %
    Favored  : 78.67 %
  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:  1.98 (0.30), residues: 735
  helix:  2.35 (0.29), residues: 321
  sheet:  1.68 (0.39), residues: 163
  loop : -0.32 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 472 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.020   0.001   TYR C 106 
 ARG   0.002   0.000   ARG A 106 

*********************** 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
  116 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A  299 TYR cc_start: 0.7016 (p90) cc_final: 0.6544 (m-80)
REVERT: B    3 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7848 (mp10)
REVERT: B   18 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8456 (mm)
REVERT: C   33 THR cc_start: 0.9190 (m) cc_final: 0.8977 (m)
REVERT: C   43 LYS cc_start: 0.8854 (ptpt) cc_final: 0.8564 (mtmm)
  outliers start: 14
  outliers final: 11
  residues processed: 109
  average time/residue: 1.0597
  time to fit residues: 123.1153
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  : 0.652 
-------------------------------------------------------------------------------
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    7 SER
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:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0070
   chunk 5 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7002

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

Flipped N/Q/H residues before XYZ refinement:
B 119 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.086274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.069855 restraints weight = 24150.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 2.87
r_work: 0.2832 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2832
-------------------------------------------------------------------------------
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 = 0.43   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:          0.3880

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= 0.180
  Angle     :  0.564   8.702   8469  Z= 0.289
  Chirality :  0.042   0.167    919
  Planarity :  0.003   0.038   1040
  Dihedral  :  8.197  56.121   1008
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.23 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.43 %
    Favored  : 78.36 %
  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:  1.98 (0.30), residues: 735
  helix:  2.35 (0.29), residues: 321
  sheet:  1.63 (0.38), residues: 164
  loop : -0.31 (0.37), residues: 250

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   0.020   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
  116 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.629 
Fit side-chains
REVERT: A  299 TYR cc_start: 0.7042 (p90) cc_final: 0.6579 (m-80)
REVERT: B    3 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7827 (mp10)
REVERT: B   18 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8434 (mm)
REVERT: C   43 LYS cc_start: 0.8873 (ptpt) cc_final: 0.8596 (mtmm)
REVERT: C   89 ASP cc_start: 0.8181 (m-30) cc_final: 0.7733 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 110
  average time/residue: 1.0030
  time to fit residues: 116.8381
Evaluate side-chains
  112 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
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 50 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0030
   chunk 13 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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 = 0.3294 r_free = 0.3294 target = 0.086471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.070419 restraints weight = 20447.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.65
r_work: 0.2853 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.3918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6242  Z= 0.175
  Angle     :  0.564   8.669   8469  Z= 0.289
  Chirality :  0.042   0.156    919
  Planarity :  0.003   0.038   1040
  Dihedral  :  8.021  53.571   1008
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.09 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.43 %
    Favored  : 78.36 %
  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:  1.97 (0.30), residues: 735
  helix:  2.38 (0.28), residues: 321
  sheet:  1.62 (0.38), residues: 164
  loop : -0.37 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 472 
 HIS   0.002   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 B  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4932.66 seconds
wall clock time: 86 minutes 59.57 seconds (5219.57 seconds total)