Starting phenix.real_space_refine
on Tue Feb 11 13:39:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bur_44917/02_2025/9bur_44917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bur_44917/02_2025/9bur_44917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bur_44917/02_2025/9bur_44917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bur_44917/02_2025/9bur_44917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bur_44917/02_2025/9bur_44917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bur_44917/02_2025/9bur_44917.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.087
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      27      5.16       5
     C    3842      2.51       5
     N     977      2.21       5
     O    1030      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 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: 5877
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5423
          Classifications: {'peptide': 663}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 33, 'TRANS': 629}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 1, 'ARG:plan': 4, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 50
    Chain: "B"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 333
          Classifications: {'peptide': 42}
          Link IDs: {'PTRANS': 4, 'TRANS': 37}
          Chain breaks: 2
    Chain: "d"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 93
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 93
          Unusual residues: {'CLR': 1, 'NAG': 2, 'POV': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.19, per 1000 atoms: 0.71
  Number of scatterers: 5877
  At special positions: 0
  Unit cell: (86.32, 92.96, 102.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P       1     15.00
     O    1030      8.00
     N     977      7.00
     C    3842      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 450 " 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
  Links applied
    BETA1-4
      " NAG d   1 " - " NAG d   2 "
    NAG-ASN
      " NAG A1201 " - " ASN A 550 "
      " NAG A1202 " - " ASN A 605 "
      " NAG d   1 " - " ASN A 570 "
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 741.0 milliseconds
  

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1336

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 3 sheets defined
      52.3% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 39
      removed outlier: 3.868A  pdb=" N   LYS A  36 " --> pdb=" O   SER A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 61 through 77
      removed outlier: 3.619A  pdb=" N   PHE A  67 " --> pdb=" O   SER A  63 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 82
      removed outlier: 3.771A  pdb=" N   GLN A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 92
    Processing helix  chain 'A' and resid 111 through 132
      removed outlier: 3.825A  pdb=" N   LEU A 117 " --> pdb=" O   ASP A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 152
      removed outlier: 3.615A  pdb=" N   VAL A 140 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
      Proline residue:  A 145  - end of helix
    Processing helix  chain 'A' and resid 153 through 157
      removed outlier: 3.650A  pdb=" N   TRP A 157 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 171
      removed outlier: 3.639A  pdb=" N   GLY A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 187
      removed outlier: 3.621A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 218
      removed outlier: 3.899A  pdb=" N   LEU A 203 " --> pdb=" O   ASN A 199 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 225
      removed outlier: 3.603A  pdb=" N   GLU A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 244
      removed outlier: 5.641A  pdb=" N   TRP A 236 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   LEU A 237 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE A 238 " --> pdb=" O   HIS A 235 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   SER A 239 " --> pdb=" O   TRP A 236 " (cutoff:3.500A)
      Proline residue:  A 240  - end of helix
      removed outlier: 3.655A  pdb=" N   LEU A 244 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 254
      removed outlier: 3.808A  pdb=" N   LEU A 252 " --> pdb=" O   GLU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 264
    Processing helix  chain 'A' and resid 275 through 294
      removed outlier: 3.614A  pdb=" N   HIS A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   GLN A 292 " --> pdb=" O   CYS A 288 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   PHE A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 307
      removed outlier: 3.690A  pdb=" N   LEU A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER A 307 " --> pdb=" O   MET A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 311
    Processing helix  chain 'A' and resid 316 through 321
    Processing helix  chain 'A' and resid 326 through 330
      removed outlier: 4.015A  pdb=" N   GLN A 329 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 362
    Processing helix  chain 'A' and resid 362 through 377
      removed outlier: 3.702A  pdb=" N   LEU A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU A 375 " --> pdb=" O   LEU A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 383
      removed outlier: 5.289A  pdb=" N   HIS A 381 " --> pdb=" O   PRO A 378 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   PHE A 382 " --> pdb=" O   TYR A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 455
    Processing helix  chain 'A' and resid 456 through 459
      removed outlier: 3.767A  pdb=" N   ASN A 459 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 456 through 459'
    Processing helix  chain 'A' and resid 506 through 511
      removed outlier: 3.648A  pdb=" N   LEU A 509 " --> pdb=" O   LEU A 506 " (cutoff:3.500A)
      Proline residue:  A 511  - end of helix
    Processing helix  chain 'A' and resid 512 through 523
    Processing helix  chain 'A' and resid 605 through 612
    Processing helix  chain 'A' and resid 614 through 619
    Processing helix  chain 'A' and resid 654 through 669
      removed outlier: 4.008A  pdb=" N   THR A 658 " --> pdb=" O   PRO A 654 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ARG A 662 " --> pdb=" O   THR A 658 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLN A 667 " --> pdb=" O   GLN A 663 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLU A 668 " --> pdb=" O   GLN A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 708
      removed outlier: 3.682A  pdb=" N   SER A 695 " --> pdb=" O   VAL A 691 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE A 696 " --> pdb=" O   PHE A 692 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR A 699 " --> pdb=" O   SER A 695 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU A 706 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE A 707 " --> pdb=" O   LEU A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 724
      removed outlier: 3.747A  pdb=" N   GLU A 719 " --> pdb=" O   GLN A 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 97
      removed outlier: 3.528A  pdb=" N   ARG B  94 " --> pdb=" O   GLN B  90 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B  96 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 479 through 480
      removed outlier: 6.404A  pdb=" N   TYR A 466 " --> pdb=" O   ILE A 413 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ILE A 413 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ASP A 468 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   VAL A 411 " --> pdb=" O   ASP A 468 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   TRP A 470 " --> pdb=" O   GLN A 409 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ILE A 413 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   TYR A 425 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 534
      removed outlier: 6.671A  pdb=" N   MET A 600 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   LEU A 555 " --> pdb=" O   MET A 600 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   VAL A 602 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   ILE A 553 " --> pdb=" O   VAL A 602 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   VAL A 604 " --> pdb=" O   THR A 551 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   THR A 551 " --> pdb=" O   VAL A 604 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   THR A 551 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 539 through 543
      removed outlier: 3.628A  pdb=" N   VAL A 560 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)

    228 hydrogen bonds defined for protein.
    651 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: 1.55

  Time building geometry restraints manager: 1.70 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: 893
        1.31 -     1.43: 1774
        1.43 -     1.56: 3331
        1.56 -     1.68: 2
        1.68 -     1.81: 44
  Bond restraints: 6044
  Sorted by residual:
  bond pdb=" C29 POV A1204 "
       pdb="C210 POV A1204 "
    ideal  model  delta    sigma   weight residual
    1.333  1.529 -0.196 2.00e-02 2.50e+03 9.61e+01
  bond pdb=" C   VAL B  45 "
       pdb=" N   VAL B  46 "
    ideal  model  delta    sigma   weight residual
    1.333  1.406 -0.073 1.29e-02 6.01e+03 3.20e+01
  bond pdb=" N   ARG A 680 "
       pdb=" CA  ARG A 680 "
    ideal  model  delta    sigma   weight residual
    1.459  1.411  0.048 1.18e-02 7.18e+03 1.66e+01
  bond pdb=" C   ARG A 680 "
       pdb=" O   ARG A 680 "
    ideal  model  delta    sigma   weight residual
    1.236  1.195  0.042 1.16e-02 7.43e+03 1.30e+01
  bond pdb=" C31 POV A1204 "
       pdb=" O31 POV A1204 "
    ideal  model  delta    sigma   weight residual
    1.327  1.395 -0.068 2.00e-02 2.50e+03 1.14e+01
  ... (remaining 6039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.18: 8146
        4.18 -     8.36: 54
        8.36 -    12.55: 5
       12.55 -    16.73: 2
       16.73 -    20.91: 1
  Bond angle restraints: 8208
  Sorted by residual:
  angle pdb=" N   ARG A 680 "
        pdb=" CA  ARG A 680 "
        pdb=" C   ARG A 680 "
      ideal   model   delta    sigma   weight residual
     111.03   99.41   11.62 1.11e+00 8.12e-01 1.10e+02
  angle pdb=" O13 POV A1204 "
        pdb=" P   POV A1204 "
        pdb=" O14 POV A1204 "
      ideal   model   delta    sigma   weight residual
     121.11  100.20   20.91 3.00e+00 1.11e-01 4.86e+01
  angle pdb=" N   PRO A 654 "
        pdb=" CA  PRO A 654 "
        pdb=" CB  PRO A 654 "
      ideal   model   delta    sigma   weight residual
     103.51  109.76   -6.25 9.60e-01 1.09e+00 4.24e+01
  angle pdb=" C28 POV A1204 "
        pdb=" C29 POV A1204 "
        pdb="C210 POV A1204 "
      ideal   model   delta    sigma   weight residual
     127.79  111.92   15.87 3.00e+00 1.11e-01 2.80e+01
  angle pdb=" N   GLN B  40 "
        pdb=" CA  GLN B  40 "
        pdb=" C   GLN B  40 "
      ideal   model   delta    sigma   weight residual
     114.75  108.62    6.13 1.26e+00 6.30e-01 2.37e+01
  ... (remaining 8203 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.29: 3225
       16.29 -    32.57: 327
       32.57 -    48.86: 75
       48.86 -    65.14: 21
       65.14 -    81.43: 5
  Dihedral angle restraints: 3653
    sinusoidal: 1581
      harmonic: 2072
  Sorted by residual:
  dihedral pdb=" CA  PRO A 324 "
           pdb=" C   PRO A 324 "
           pdb=" N   ARG A 325 "
           pdb=" CA  ARG A 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.99  -28.01     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  THR A 653 "
           pdb=" C   THR A 653 "
           pdb=" N   PRO A 654 "
           pdb=" CA  PRO A 654 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.90   25.10     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  GLY A 429 "
           pdb=" C   GLY A 429 "
           pdb=" N   VAL A 430 "
           pdb=" CA  VAL A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.30  -24.70     0      5.00e+00 4.00e-02 2.44e+01
  ... (remaining 3650 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 626
       0.052 -    0.103: 213
       0.103 -    0.155: 43
       0.155 -    0.206: 12
       0.206 -    0.258: 2
  Chirality restraints: 896
  Sorted by residual:
  chirality pdb=" CA  PRO A 654 "
            pdb=" N   PRO A 654 "
            pdb=" C   PRO A 654 "
            pdb=" CB  PRO A 654 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ARG A 680 "
            pdb=" N   ARG A 680 "
            pdb=" C   ARG A 680 "
            pdb=" CB  ARG A 680 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  VAL A 691 "
            pdb=" CA  VAL A 691 "
            pdb=" CG1 VAL A 691 "
            pdb=" CG2 VAL A 691 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.83e-01
  ... (remaining 893 not shown)

  Planarity restraints: 1024
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV A1204 "   -0.087 2.00e-02 2.50e+03   8.73e-02 7.62e+01
        pdb=" C29 POV A1204 "    0.084 2.00e-02 2.50e+03
        pdb="C210 POV A1204 "    0.091 2.00e-02 2.50e+03
        pdb="C211 POV A1204 "   -0.088 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 307 "   -0.053 5.00e-02 4.00e+02   7.84e-02 9.84e+00
        pdb=" N   PRO A 308 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 308 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 308 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 679 "    0.015 2.00e-02 2.50e+03   3.10e-02 9.63e+00
        pdb=" C   GLU A 679 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   GLU A 679 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A 680 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1021 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1301
        2.77 -     3.30: 5017
        3.30 -     3.84: 9827
        3.84 -     4.37: 12261
        4.37 -     4.90: 20678
  Nonbonded interactions: 49084
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 586 "
            pdb=" O   LYS B  39 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   SER A 228 "
            pdb=" NE2 HIS A 256 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   SER A 695 "
            pdb=" OG1 THR A 699 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OE1 GLN A 206 "
            pdb=" OH  TYR A 370 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   LEU A 280 "
            pdb=" OG  SER A 284 "
     model   vdw
     2.313 3.040
  ... (remaining 49079 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.130
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
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   0.196   6044  Z= 0.497
  Angle     :  1.037  20.909   8208  Z= 0.556
  Chirality :  0.055   0.258    896
  Planarity :  0.009   0.087   1021
  Dihedral  : 14.369  81.429   2314
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  5.19 %
    Favored  : 94.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.84 (0.24), residues: 693
  helix: -4.48 (0.12), residues: 325
  sheet: -2.44 (0.50), residues: 76
  loop : -1.54 (0.32), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 198 
 HIS   0.010   0.002   HIS A 526 
 PHE   0.013   0.002   PHE A 382 
 TYR   0.031   0.003   TYR B  97 
 ARG   0.012   0.001   ARG A 683 

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8235 (mm) cc_final: 0.7939 (mm)
REVERT: A  422 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7012 (mm-30)
REVERT: A  459 ASN cc_start: 0.8152 (m-40) cc_final: 0.7028 (t0)
REVERT: A  475 ASP cc_start: 0.8054 (m-30) cc_final: 0.7795 (m-30)
REVERT: A  517 GLN cc_start: 0.7565 (tp-100) cc_final: 0.7295 (tp-100)
REVERT: A  569 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7720 (tppt)
REVERT: A  680 ARG cc_start: 0.6212 (mmm-85) cc_final: 0.5909 (mtt180)
REVERT: A  689 LEU cc_start: 0.7896 (tt) cc_final: 0.7302 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 106
  average time/residue: 1.3607
  time to fit residues: 150.8581
Evaluate side-chains
  71 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  602 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 18 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0970
   chunk 28 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 235 HIS
A 292 GLN
A 354 GLN
A 404 HIS
A 408 HIS
A 409 GLN
A 440 HIS
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 526 HIS
A 674 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.149979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.120474 restraints weight = 6648.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.53
r_work: 0.3075 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6044  Z= 0.188
  Angle     :  0.557   6.310   8208  Z= 0.289
  Chirality :  0.040   0.150    896
  Planarity :  0.006   0.062   1021
  Dihedral  :  7.929  57.914    959
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.99 %
    Favored  : 85.23 %
  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: -3.27 (0.27), residues: 693
  helix: -2.82 (0.20), residues: 349
  sheet: -1.98 (0.55), residues: 72
  loop : -0.93 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 256 
 PHE   0.012   0.001   PHE A 286 
 TYR   0.016   0.001   TYR A 162 
 ARG   0.004   0.001   ARG A 683 

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8313 (mm) cc_final: 0.8019 (mm)
REVERT: A  422 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7273 (mm-30)
REVERT: A  459 ASN cc_start: 0.8369 (m-40) cc_final: 0.7279 (t0)
REVERT: A  475 ASP cc_start: 0.8368 (m-30) cc_final: 0.8148 (m-30)
REVERT: A  569 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7678 (tppt)
REVERT: A  612 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.5948 (mp0)
REVERT: A  689 LEU cc_start: 0.8605 (tt) cc_final: 0.7917 (mp)
REVERT: A  713 LEU cc_start: 0.7740 (mt) cc_final: 0.7480 (mm)
  outliers start: 11
  outliers final: 3
  residues processed: 82
  average time/residue: 1.2882
  time to fit residues: 110.7818
Evaluate side-chains
  68 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  612 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 66 optimal weight:    0.1980
   chunk 41 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 38 optimal weight:    0.2980
   chunk 40 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
A 479 GLN
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.141805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.109968 restraints weight = 6887.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.64
r_work: 0.3218 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6044  Z= 0.179
  Angle     :  0.512   7.438   8208  Z= 0.260
  Chirality :  0.040   0.147    896
  Planarity :  0.005   0.054   1021
  Dihedral  :  7.144  59.641    959
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.47 %
    Favored  : 83.93 %
  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: -1.84 (0.30), residues: 693
  helix: -1.51 (0.25), residues: 346
  sheet: -1.46 (0.56), residues: 68
  loop : -0.44 (0.38), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.015   0.001   PHE A 286 
 TYR   0.014   0.001   TYR A 162 
 ARG   0.004   0.000   ARG A 108 

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8317 (mm) cc_final: 0.8092 (mm)
REVERT: A  416 ARG cc_start: 0.8374 (ttp-170) cc_final: 0.8153 (ttm170)
REVERT: A  422 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7304 (mm-30)
REVERT: A  459 ASN cc_start: 0.8412 (m-40) cc_final: 0.7370 (t0)
REVERT: A  475 ASP cc_start: 0.8356 (m-30) cc_final: 0.8135 (m-30)
REVERT: A  554 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7530 (tt0)
REVERT: A  569 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7828 (tppt)
REVERT: A  689 LEU cc_start: 0.8686 (tt) cc_final: 0.7972 (mp)
  outliers start: 16
  outliers final: 3
  residues processed: 81
  average time/residue: 1.2466
  time to fit residues: 106.1581
Evaluate side-chains
  68 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  602 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 45 optimal weight:    0.2980
   chunk 8 optimal weight:    0.0170
   chunk 6 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 354 GLN
A 479 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.158038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.126933 restraints weight = 6810.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.61
r_work: 0.3068 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6044  Z= 0.167
  Angle     :  0.502   8.563   8208  Z= 0.250
  Chirality :  0.040   0.181    896
  Planarity :  0.004   0.052   1021
  Dihedral  :  6.801  58.760    959
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.75 %
    Favored  : 82.47 %
  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: -1.19 (0.31), residues: 693
  helix: -0.80 (0.27), residues: 342
  sheet: -1.42 (0.58), residues: 70
  loop : -0.31 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 198 
 HIS   0.003   0.001   HIS A 256 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.014   0.001   TYR A 162 
 ARG   0.003   0.000   ARG A 108 

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7178 (mttm)
REVERT: A  104 LEU cc_start: 0.8283 (mm) cc_final: 0.8019 (mm)
REVERT: A  416 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7956 (ttm170)
REVERT: A  422 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7062 (mm-30)
REVERT: A  459 ASN cc_start: 0.8345 (m-40) cc_final: 0.7189 (t0)
REVERT: A  475 ASP cc_start: 0.8240 (m-30) cc_final: 0.7966 (m-30)
REVERT: A  554 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7473 (tt0)
REVERT: A  569 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7556 (tppt)
REVERT: A  575 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6932 (mp0)
REVERT: A  602 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8584 (p)
REVERT: A  680 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6472 (mtp85)
REVERT: A  689 LEU cc_start: 0.8427 (tt) cc_final: 0.7707 (mp)
  outliers start: 11
  outliers final: 4
  residues processed: 77
  average time/residue: 1.1579
  time to fit residues: 94.2042
Evaluate side-chains
  76 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 3 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0870
   chunk 57 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0070
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 354 GLN
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.158736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.127563 restraints weight = 6757.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.65
r_work: 0.3068 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6044  Z= 0.149
  Angle     :  0.483   8.372   8208  Z= 0.241
  Chirality :  0.039   0.153    896
  Planarity :  0.004   0.052   1021
  Dihedral  :  6.578  59.873    959
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.07 %
    Favored  : 81.82 %
  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: -0.72 (0.32), residues: 693
  helix: -0.38 (0.28), residues: 347
  sheet: -1.19 (0.59), residues: 69
  loop : -0.14 (0.38), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 198 
 HIS   0.003   0.001   HIS A 256 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.014   0.001   TYR A 285 
 ARG   0.002   0.000   ARG A 276 

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7686 (ttpp) cc_final: 0.7273 (mttm)
REVERT: A  104 LEU cc_start: 0.8335 (mm) cc_final: 0.8094 (mm)
REVERT: A  346 LYS cc_start: 0.8671 (pttm) cc_final: 0.8249 (pmtt)
REVERT: A  416 ARG cc_start: 0.8244 (ttp-170) cc_final: 0.8028 (ttm170)
REVERT: A  422 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7049 (mm-30)
REVERT: A  459 ASN cc_start: 0.8336 (m-40) cc_final: 0.7178 (t0)
REVERT: A  541 GLU cc_start: 0.8232 (tt0) cc_final: 0.7838 (tp30)
REVERT: A  554 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7486 (tt0)
REVERT: A  569 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7626 (tppt)
REVERT: A  575 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6956 (mp0)
REVERT: A  680 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6486 (mtp85)
REVERT: A  689 LEU cc_start: 0.8444 (tt) cc_final: 0.7746 (mp)
  outliers start: 13
  outliers final: 5
  residues processed: 75
  average time/residue: 1.1657
  time to fit residues: 92.2487
Evaluate side-chains
  71 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0970
   chunk 52 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 9 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
A 526 HIS
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.156295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.124865 restraints weight = 6694.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.66
r_work: 0.3013 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6044  Z= 0.213
  Angle     :  0.514   8.520   8208  Z= 0.256
  Chirality :  0.041   0.163    896
  Planarity :  0.004   0.053   1021
  Dihedral  :  6.543  63.626    958
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.21 %
    Favored  : 80.52 %
  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: -0.61 (0.32), residues: 693
  helix: -0.30 (0.28), residues: 351
  sheet: -1.14 (0.57), residues: 74
  loop : -0.02 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.013   0.001   TYR A 162 
 ARG   0.002   0.000   ARG A 359 

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.630 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7705 (ttpp) cc_final: 0.7273 (mttm)
REVERT: A  104 LEU cc_start: 0.8353 (mm) cc_final: 0.8109 (mm)
REVERT: A  346 LYS cc_start: 0.8740 (pttm) cc_final: 0.8232 (pmtt)
REVERT: A  416 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.8064 (ttm170)
REVERT: A  422 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7062 (mm-30)
REVERT: A  435 ARG cc_start: 0.8717 (mtp180) cc_final: 0.7517 (mmp80)
REVERT: A  475 ASP cc_start: 0.8297 (m-30) cc_final: 0.8019 (m-30)
REVERT: A  541 GLU cc_start: 0.8267 (tt0) cc_final: 0.7896 (tp30)
REVERT: A  554 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7530 (tt0)
REVERT: A  569 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7626 (tppt)
REVERT: A  575 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6991 (mp0)
REVERT: A  689 LEU cc_start: 0.8474 (tt) cc_final: 0.7755 (mp)
  outliers start: 14
  outliers final: 7
  residues processed: 73
  average time/residue: 1.1175
  time to fit residues: 86.2550
Evaluate side-chains
  70 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0770
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
A 526 HIS
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.156873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.125649 restraints weight = 6796.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.67
r_work: 0.3064 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6044  Z= 0.180
  Angle     :  0.496   8.571   8208  Z= 0.246
  Chirality :  0.040   0.159    896
  Planarity :  0.004   0.051   1021
  Dihedral  :  6.418  64.032    958
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.37 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.32), residues: 693
  helix: -0.04 (0.28), residues: 346
  sheet: -1.05 (0.57), residues: 74
  loop :  0.03 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.012   0.001   PHE A 286 
 TYR   0.014   0.001   TYR A 285 
 ARG   0.002   0.000   ARG A 276 

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7209 (mttm)
REVERT: A  104 LEU cc_start: 0.8360 (mm) cc_final: 0.8120 (mm)
REVERT: A  346 LYS cc_start: 0.8743 (pttm) cc_final: 0.8263 (pmtt)
REVERT: A  416 ARG cc_start: 0.8228 (ttp-170) cc_final: 0.8024 (ttm170)
REVERT: A  422 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7073 (mm-30)
REVERT: A  541 GLU cc_start: 0.8241 (tt0) cc_final: 0.7872 (tp30)
REVERT: A  554 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7480 (tt0)
REVERT: A  569 LYS cc_start: 0.8064 (ttpp) cc_final: 0.7610 (tppt)
REVERT: A  575 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6963 (mp0)
REVERT: A  680 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6485 (mtp85)
REVERT: A  689 LEU cc_start: 0.8436 (tt) cc_final: 0.7701 (mp)
  outliers start: 12
  outliers final: 5
  residues processed: 72
  average time/residue: 1.0787
  time to fit residues: 82.2999
Evaluate side-chains
  67 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 20 optimal weight:    0.2980
   chunk 13 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
A 526 HIS
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.157318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.125960 restraints weight = 6715.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.69
r_work: 0.3017 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6044  Z= 0.178
  Angle     :  0.493   8.032   8208  Z= 0.245
  Chirality :  0.040   0.157    896
  Planarity :  0.004   0.049   1021
  Dihedral  :  6.348  64.416    958
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.02 %
    Favored  : 80.52 %
  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: -0.22 (0.32), residues: 693
  helix:  0.10 (0.28), residues: 346
  sheet: -0.98 (0.57), residues: 74
  loop :  0.05 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.013   0.001   TYR A 162 
 ARG   0.002   0.000   ARG A 276 

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7608 (ttpp) cc_final: 0.7147 (mttm)
REVERT: A  104 LEU cc_start: 0.8313 (mm) cc_final: 0.8065 (mm)
REVERT: A  346 LYS cc_start: 0.8741 (pttm) cc_final: 0.8247 (pmtt)
REVERT: A  416 ARG cc_start: 0.8188 (ttp-170) cc_final: 0.7984 (ttm170)
REVERT: A  422 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7029 (mm-30)
REVERT: A  475 ASP cc_start: 0.8269 (m-30) cc_final: 0.7926 (m-30)
REVERT: A  541 GLU cc_start: 0.8258 (tt0) cc_final: 0.7844 (tp30)
REVERT: A  554 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7483 (tt0)
REVERT: A  569 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7554 (tppt)
REVERT: A  575 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6977 (mp0)
REVERT: A  680 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6419 (mtp85)
REVERT: A  689 LEU cc_start: 0.8367 (tt) cc_final: 0.7628 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 71
  average time/residue: 1.1217
  time to fit residues: 84.2005
Evaluate side-chains
  68 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
A 526 HIS
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.156799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.125471 restraints weight = 6669.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.67
r_work: 0.3036 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6044  Z= 0.194
  Angle     :  0.502   7.992   8208  Z= 0.250
  Chirality :  0.040   0.158    896
  Planarity :  0.004   0.050   1021
  Dihedral  :  6.340  65.464    958
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.83 %
    Favored  : 79.38 %
  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: -0.11 (0.32), residues: 693
  helix:  0.20 (0.28), residues: 346
  sheet: -0.86 (0.58), residues: 74
  loop :  0.06 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.013   0.001   TYR A 162 
 ARG   0.002   0.000   ARG A 276 

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7679 (ttpp) cc_final: 0.7218 (mttm)
REVERT: A  104 LEU cc_start: 0.8375 (mm) cc_final: 0.8119 (mm)
REVERT: A  346 LYS cc_start: 0.8718 (pttm) cc_final: 0.8275 (pmtt)
REVERT: A  416 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7958 (ttm170)
REVERT: A  422 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7122 (mm-30)
REVERT: A  475 ASP cc_start: 0.8244 (m-30) cc_final: 0.7885 (m-30)
REVERT: A  541 GLU cc_start: 0.8232 (tt0) cc_final: 0.7842 (tp30)
REVERT: A  554 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7489 (tt0)
REVERT: A  569 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7543 (tppt)
REVERT: A  575 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7012 (mp0)
REVERT: A  680 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6462 (mtp85)
REVERT: A  689 LEU cc_start: 0.8418 (tt) cc_final: 0.7679 (mp)
  outliers start: 11
  outliers final: 7
  residues processed: 68
  average time/residue: 1.1512
  time to fit residues: 82.6043
Evaluate side-chains
  69 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    0.2980
   chunk 40 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0060
   chunk 6 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0770
   overall best weight:    0.3554

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
A 526 HIS
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.160237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.129496 restraints weight = 6733.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.66
r_work: 0.3113 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6044  Z= 0.129
  Angle     :  0.465   7.891   8208  Z= 0.232
  Chirality :  0.039   0.140    896
  Planarity :  0.004   0.048   1021
  Dihedral  :  6.067  63.379    958
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 19.64 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.32), residues: 693
  helix:  0.54 (0.29), residues: 345
  sheet: -0.77 (0.58), residues: 74
  loop :  0.13 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 257 
 HIS   0.003   0.001   HIS A 256 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.013   0.001   TYR A 162 
 ARG   0.002   0.000   ARG A 276 

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7225 (mttm)
REVERT: A  104 LEU cc_start: 0.8410 (mm) cc_final: 0.8181 (mm)
REVERT: A  346 LYS cc_start: 0.8732 (pttm) cc_final: 0.8315 (pmtt)
REVERT: A  422 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7168 (mm-30)
REVERT: A  475 ASP cc_start: 0.8113 (m-30) cc_final: 0.7771 (m-30)
REVERT: A  541 GLU cc_start: 0.8190 (tt0) cc_final: 0.7870 (tp30)
REVERT: A  569 LYS cc_start: 0.8123 (ttpp) cc_final: 0.7623 (tppt)
REVERT: A  680 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6508 (mtp85)
REVERT: A  689 LEU cc_start: 0.8444 (tt) cc_final: 0.7704 (mp)
  outliers start: 7
  outliers final: 4
  residues processed: 71
  average time/residue: 1.0960
  time to fit residues: 82.6224
Evaluate side-chains
  65 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 27 optimal weight:    0.3980
   chunk 64 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
A 526 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.158132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.127197 restraints weight = 6761.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.64
r_work: 0.3080 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6044  Z= 0.173
  Angle     :  0.491   7.418   8208  Z= 0.244
  Chirality :  0.040   0.151    896
  Planarity :  0.004   0.049   1021
  Dihedral  :  6.104  64.557    958
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 20.13 %
    Favored  : 79.06 %
  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:  0.26 (0.32), residues: 693
  helix:  0.56 (0.29), residues: 346
  sheet: -0.67 (0.58), residues: 74
  loop :  0.14 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 257 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.014   0.001   TYR A 285 
 ARG   0.002   0.000   ARG A 276 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4260.81 seconds
wall clock time: 76 minutes 18.41 seconds (4578.41 seconds total)