Starting phenix.real_space_refine
on Sat May 10 08:14:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8phw_17677/05_2025/8phw_17677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8phw_17677/05_2025/8phw_17677.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8phw_17677/05_2025/8phw_17677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8phw_17677/05_2025/8phw_17677.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8phw_17677/05_2025/8phw_17677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8phw_17677/05_2025/8phw_17677.cif"
  }
  resolution = 3.6
  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=   0.022
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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    3500      2.51       5
     N     847      2.21       5
     O     976      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5359
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3528
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 15, 'TRANS': 438}
          Chain breaks: 7
    Chain: "H"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 972
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 3, 'TRANS': 124}
    Chain: "L"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 800
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'FY5': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.64, per 1000 atoms: 0.87
  Number of scatterers: 5359
  At special positions: 0
  Unit cell: (87.72, 94.86, 104.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O     976      8.00
     N     847      7.00
     C    3500      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 530 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 465 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 599 " - pdb=" SG  CYS A 613 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.04

  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: 1.44
  Conformation dependent library (CDL) restraints added in 756.9 milliseconds
  

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1246

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 6 sheets defined
      46.4% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 52
      removed outlier: 3.742A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LYS A  41 " --> pdb=" O   SER A  37 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ALA A  45 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   ILE A  46 " --> pdb=" O   THR A  42 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER A  50 " --> pdb=" O   ILE A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 80
      removed outlier: 3.860A  pdb=" N   PHE A  68 " --> pdb=" O   SER A  64 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   PHE A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   GLU A  74 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASN A  77 " --> pdb=" O   PHE A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 117
      removed outlier: 4.217A  pdb=" N   GLY A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   CYS A 101 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   PHE A 102 " --> pdb=" O   GLY A  98 " (cutoff:3.500A)
      Proline residue:  A 114  - end of helix
      removed outlier: 3.612A  pdb=" N   PHE A 117 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 185
      removed outlier: 3.718A  pdb=" N   GLY A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 199
      removed outlier: 3.743A  pdb=" N   LEU A 193 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 3.891A  pdb=" N   MET A 217 " --> pdb=" O   ASN A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 4.153A  pdb=" N   ILE A 221 " --> pdb=" O   MET A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 245
    Processing helix  chain 'A' and resid 257 through 274
      removed outlier: 4.055A  pdb=" N   ASN A 261 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 340 through 366
      removed outlier: 3.595A  pdb=" N   GLN A 348 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   SER A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   PHE A 360 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   LYS A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 381
    Processing helix  chain 'A' and resid 381 through 400
      removed outlier: 3.875A  pdb=" N   GLY A 394 " --> pdb=" O   MET A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 423
      removed outlier: 3.522A  pdb=" N   ALA A 408 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 487
    Processing helix  chain 'A' and resid 527 through 559
      removed outlier: 3.685A  pdb=" N   THR A 531 " --> pdb=" O   ASP A 527 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   TYR A 535 " --> pdb=" O   THR A 531 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   PHE A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A 550 " --> pdb=" O   PHE A 546 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   GLY A 551 " --> pdb=" O   PHE A 547 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR A 553 " --> pdb=" O   ALA A 549 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER A 554 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   VAL A 556 " --> pdb=" O   GLY A 552 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   MET A 557 " --> pdb=" O   THR A 553 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE A 559 " --> pdb=" O   HIS A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 597
      Proline residue:  A 588  - end of helix
    Processing helix  chain 'A' and resid 617 through 646
      removed outlier: 3.665A  pdb=" N   LEU A 639 " --> pdb=" O   SER A 635 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 434 through 435
      removed outlier: 7.052A  pdb=" N   SER A 434 " --> pdb=" O   THR A 480 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   HIS A 520 " --> pdb=" O   CYS A 474 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10
      removed outlier: 4.208A  pdb=" N   GLN H   6 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER H  28 " --> pdb=" O   GLN H   6 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 54
      removed outlier: 6.837A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 55
      removed outlier: 3.777A  pdb=" N   SER L  54 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR L  50 " --> pdb=" O   SER L  54 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55
      removed outlier: 3.777A  pdb=" N   SER L  54 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR L  50 " --> pdb=" O   SER L  54 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    264 hydrogen bonds defined for protein.
    750 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: 1.38

  Time building geometry restraints manager: 1.66 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 822
        1.32 -     1.45: 1624
        1.45 -     1.57: 2991
        1.57 -     1.70: 1
        1.70 -     1.82: 53
  Bond restraints: 5491
  Sorted by residual:
  bond pdb=" O20 FY5 A 701 "
       pdb=" S21 FY5 A 701 "
    ideal  model  delta    sigma   weight residual
    1.673  1.603  0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C   THR A 186 "
       pdb=" N   PRO A 187 "
    ideal  model  delta    sigma   weight residual
    1.331  1.351 -0.020 7.90e-03 1.60e+04 6.28e+00
  bond pdb=" C18 FY5 A 701 "
       pdb=" O20 FY5 A 701 "
    ideal  model  delta    sigma   weight residual
    1.372  1.421 -0.049 2.00e-02 2.50e+03 6.04e+00
  bond pdb=" N   VAL L  34 "
       pdb=" CA  VAL L  34 "
    ideal  model  delta    sigma   weight residual
    1.459  1.441  0.018 1.25e-02 6.40e+03 2.09e+00
  bond pdb=" C   SER H  36 "
       pdb=" N   ILE H  37 "
    ideal  model  delta    sigma   weight residual
    1.334  1.316  0.017 1.24e-02 6.50e+03 1.98e+00
  ... (remaining 5486 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 7000
        1.36 -     2.72: 372
        2.72 -     4.07: 56
        4.07 -     5.43: 18
        5.43 -     6.79: 6
  Bond angle restraints: 7452
  Sorted by residual:
  angle pdb=" N   ILE A 428 "
        pdb=" CA  ILE A 428 "
        pdb=" C   ILE A 428 "
      ideal   model   delta    sigma   weight residual
     112.83  108.67    4.16 9.90e-01 1.02e+00 1.77e+01
  angle pdb=" N   TYR H  63 "
        pdb=" CA  TYR H  63 "
        pdb=" C   TYR H  63 "
      ideal   model   delta    sigma   weight residual
     108.34  112.26   -3.92 1.31e+00 5.83e-01 8.93e+00
  angle pdb=" C   SER L  51 "
        pdb=" N   ALA L  52 "
        pdb=" CA  ALA L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  127.23   -5.69 1.91e+00 2.74e-01 8.89e+00
  angle pdb=" CA  TYR A 590 "
        pdb=" CB  TYR A 590 "
        pdb=" CG  TYR A 590 "
      ideal   model   delta    sigma   weight residual
     113.90  119.01   -5.11 1.80e+00 3.09e-01 8.05e+00
  angle pdb=" C   ASN A 403 "
        pdb=" CA  ASN A 403 "
        pdb=" CB  ASN A 403 "
      ideal   model   delta    sigma   weight residual
     110.42  115.50   -5.08 1.99e+00 2.53e-01 6.51e+00
  ... (remaining 7447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.98: 2818
       11.98 -    23.96: 279
       23.96 -    35.94: 111
       35.94 -    47.92: 36
       47.92 -    59.90: 11
  Dihedral angle restraints: 3255
    sinusoidal: 1292
      harmonic: 1963
  Sorted by residual:
  dihedral pdb=" CA  CYS A 607 "
           pdb=" C   CYS A 607 "
           pdb=" N   GLY A 608 "
           pdb=" CA  GLY A 608 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.90   27.10     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  GLY A 608 "
           pdb=" C   GLY A 608 "
           pdb=" N   THR A 609 "
           pdb=" CA  THR A 609 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.57  -25.43     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ASN A 617 "
           pdb=" C   ASN A 617 "
           pdb=" N   SER A 618 "
           pdb=" CA  SER A 618 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.20  -22.80     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 3252 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 496
       0.029 -    0.058: 229
       0.058 -    0.087: 76
       0.087 -    0.115: 37
       0.115 -    0.144: 9
  Chirality restraints: 847
  Sorted by residual:
  chirality pdb=" CA  VAL A 473 "
            pdb=" N   VAL A 473 "
            pdb=" C   VAL A 473 "
            pdb=" CB  VAL A 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.20e-01
  chirality pdb=" CA  THR A 186 "
            pdb=" N   THR A 186 "
            pdb=" C   THR A 186 "
            pdb=" CB  THR A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.97e-01
  chirality pdb=" CA  PRO A 220 "
            pdb=" N   PRO A 220 "
            pdb=" C   PRO A 220 "
            pdb=" CB  PRO A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.67e-01
  ... (remaining 844 not shown)

  Planarity restraints: 905
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 219 "   -0.038 5.00e-02 4.00e+02   5.77e-02 5.32e+00
        pdb=" N   PRO A 220 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY H 106 "   -0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO H 107 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO H 107 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H 107 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 590 "   -0.013 2.00e-02 2.50e+03   1.01e-02 2.05e+00
        pdb=" CG  TYR A 590 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 590 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 590 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 590 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 590 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 590 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 590 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 902 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 793
        2.75 -     3.29: 5508
        3.29 -     3.82: 8421
        3.82 -     4.36: 9687
        4.36 -     4.90: 16556
  Nonbonded interactions: 40965
  Sorted by model distance:
  nonbonded pdb=" O   CYS A 101 "
            pdb=" OG  SER A 269 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   ALA A 415 "
            pdb=" OG  SER A 418 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OD1 ASP L  83 "
            pdb=" OH  TYR L  87 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" NH2 ARG H  70 "
            pdb=" O   SER H  88 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   CYS A 474 "
            pdb=" N   ALA A 519 "
     model   vdw
     2.252 3.120
  ... (remaining 40960 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 group one per residue
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:             5.710
  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:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.250
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
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      :  0.005   0.070   5497  Z= 0.233
  Angle     :  0.723   6.790   7464  Z= 0.423
  Chirality :  0.041   0.144    847
  Planarity :  0.005   0.058    905
  Dihedral  : 12.284  59.901   1991
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  :  7.75 %
    Favored  : 86.06 %
  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: -3.65 (0.26), residues: 669
  helix: -1.77 (0.25), residues: 283
  sheet: -1.50 (0.57), residues: 81
  loop : -3.36 (0.26), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 254 
 HIS   0.003   0.001   HIS A 115 
 PHE   0.010   0.001   PHE A 537 
 TYR   0.025   0.002   TYR A 590 
 ARG   0.003   0.000   ARG H  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13904 (  256)
  hydrogen bonds       : angle       5.86732 (  750)
  SS BOND              : bond        0.00428 (    6)
  SS BOND              : angle       1.12052 (   12)
  covalent geometry    : bond        0.00461 ( 5491)
  covalent geometry    : angle       0.72217 ( 7452)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6160 (ttp80)
REVERT: A  170 MET cc_start: 0.7729 (ttm) cc_final: 0.7378 (ttm)
REVERT: A  218 ILE cc_start: 0.7663 (mm) cc_final: 0.7459 (tt)
REVERT: A  253 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6436 (mtm110)
REVERT: A  386 PHE cc_start: 0.8258 (t80) cc_final: 0.7730 (t80)
REVERT: A  390 MET cc_start: 0.7207 (mtm) cc_final: 0.6897 (mtm)
REVERT: A  417 MET cc_start: 0.6765 (mmm) cc_final: 0.6395 (mmm)
REVERT: A  601 LYS cc_start: 0.7751 (tttp) cc_final: 0.7317 (tttp)
REVERT: A  631 MET cc_start: 0.6745 (tpp) cc_final: 0.6223 (tpp)
REVERT: H   32 PHE cc_start: 0.8359 (t80) cc_final: 0.8126 (t80)
REVERT: L   18 ASP cc_start: 0.5539 (m-30) cc_final: 0.5334 (m-30)
REVERT: L   43 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7601 (mmtm)
  outliers start: 36
  outliers final: 16
  residues processed: 167
  average time/residue: 0.1501
  time to fit residues: 33.1033
Evaluate side-chains
  147 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  253 ARG
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue  105 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0040
   chunk 27 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.4392

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.144536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.124418 restraints weight = 9027.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.128354 restraints weight = 4461.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.130776 restraints weight = 2750.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5497  Z= 0.132
  Angle     :  0.603   7.545   7464  Z= 0.310
  Chirality :  0.042   0.297    847
  Planarity :  0.005   0.057    905
  Dihedral  :  8.106  59.016    886
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 14.46 %
    Favored  : 79.52 %
  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: -1.71 (0.30), residues: 669
  helix:  0.23 (0.30), residues: 291
  sheet: -1.02 (0.60), residues: 78
  loop : -2.62 (0.29), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.023   0.001   PHE A  73 
 TYR   0.014   0.001   TYR A 625 
 ARG   0.003   0.000   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04835 (  256)
  hydrogen bonds       : angle       4.51695 (  750)
  SS BOND              : bond        0.00426 (    6)
  SS BOND              : angle       1.12816 (   12)
  covalent geometry    : bond        0.00280 ( 5491)
  covalent geometry    : angle       0.60208 ( 7452)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 MET cc_start: 0.7665 (ttm) cc_final: 0.7439 (ttm)
REVERT: A  173 TYR cc_start: 0.7485 (m-80) cc_final: 0.7257 (m-80)
REVERT: A  217 MET cc_start: 0.7922 (mmp) cc_final: 0.7561 (mmp)
REVERT: A  253 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6715 (mtm110)
REVERT: A  386 PHE cc_start: 0.8098 (t80) cc_final: 0.7418 (t80)
REVERT: A  390 MET cc_start: 0.7205 (mtm) cc_final: 0.6844 (mtm)
REVERT: A  417 MET cc_start: 0.6699 (mmm) cc_final: 0.6363 (mmm)
REVERT: A  533 LYS cc_start: 0.7966 (mttm) cc_final: 0.7713 (mttm)
REVERT: A  545 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7850 (mm)
REVERT: A  601 LYS cc_start: 0.7569 (tttp) cc_final: 0.7199 (tttp)
REVERT: A  631 MET cc_start: 0.6743 (tpp) cc_final: 0.6236 (tpp)
REVERT: H   32 PHE cc_start: 0.8268 (t80) cc_final: 0.8035 (t80)
REVERT: L   18 ASP cc_start: 0.5998 (m-30) cc_final: 0.5686 (m-30)
REVERT: L   43 LYS cc_start: 0.7712 (mmtm) cc_final: 0.7508 (mmtm)
  outliers start: 35
  outliers final: 18
  residues processed: 153
  average time/residue: 0.1414
  time to fit residues: 29.0958
Evaluate side-chains
  144 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  253 ARG
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue  103 THR
Chi-restraints excluded: chain L residue  105 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 15 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 19 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0970
   chunk 2 optimal weight:    0.0670
   overall best weight:    0.2916

-------------------------------------------------------------------------------
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 = 0.3923 r_free = 0.3923 target = 0.148183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.128840 restraints weight = 9104.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.132519 restraints weight = 4501.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.135006 restraints weight = 2812.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5497  Z= 0.106
  Angle     :  0.559   6.960   7464  Z= 0.283
  Chirality :  0.040   0.160    847
  Planarity :  0.004   0.040    905
  Dihedral  :  6.956  59.431    877
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 17.90 %
    Favored  : 76.76 %
  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: -0.78 (0.32), residues: 669
  helix:  1.22 (0.31), residues: 296
  sheet: -0.85 (0.60), residues: 83
  loop : -2.37 (0.32), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.013   0.001   PHE A  73 
 TYR   0.012   0.001   TYR A 239 
 ARG   0.004   0.000   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03910 (  256)
  hydrogen bonds       : angle       4.11713 (  750)
  SS BOND              : bond        0.00397 (    6)
  SS BOND              : angle       0.96176 (   12)
  covalent geometry    : bond        0.00220 ( 5491)
  covalent geometry    : angle       0.55859 ( 7452)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6299 (ttp-170)
REVERT: A  386 PHE cc_start: 0.7946 (t80) cc_final: 0.7249 (t80)
REVERT: A  390 MET cc_start: 0.7052 (mtm) cc_final: 0.6759 (mtm)
REVERT: A  533 LYS cc_start: 0.7869 (mttm) cc_final: 0.7660 (mttm)
REVERT: A  545 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7836 (mm)
REVERT: A  601 LYS cc_start: 0.7248 (tttp) cc_final: 0.6959 (tttp)
REVERT: A  631 MET cc_start: 0.6682 (tpp) cc_final: 0.6221 (tpp)
  outliers start: 31
  outliers final: 19
  residues processed: 154
  average time/residue: 0.1526
  time to fit residues: 30.8232
Evaluate side-chains
  148 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain H residue   25 CYS
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue  103 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0060
   overall best weight:    1.0800

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
A 544 ASN
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.142133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.122089 restraints weight = 9285.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.125965 restraints weight = 4562.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.128544 restraints weight = 2808.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5497  Z= 0.227
  Angle     :  0.659   8.017   7464  Z= 0.336
  Chirality :  0.044   0.165    847
  Planarity :  0.004   0.046    905
  Dihedral  :  6.984  60.373    870
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 19.10 %
    Favored  : 74.35 %
  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: -0.90 (0.32), residues: 669
  helix:  1.14 (0.31), residues: 294
  sheet: -0.76 (0.61), residues: 81
  loop : -2.47 (0.31), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 254 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.015   0.001   PHE A  73 
 TYR   0.024   0.002   TYR L  50 
 ARG   0.006   0.000   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05097 (  256)
  hydrogen bonds       : angle       4.51888 (  750)
  SS BOND              : bond        0.00810 (    6)
  SS BOND              : angle       1.55080 (   12)
  covalent geometry    : bond        0.00496 ( 5491)
  covalent geometry    : angle       0.65618 ( 7452)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 134
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6300 (ttp80)
REVERT: A  173 TYR cc_start: 0.7465 (m-80) cc_final: 0.7227 (m-80)
REVERT: A  176 MET cc_start: 0.6755 (mmt) cc_final: 0.6526 (mmt)
REVERT: A  386 PHE cc_start: 0.8048 (t80) cc_final: 0.7292 (t80)
REVERT: A  390 MET cc_start: 0.7184 (mtm) cc_final: 0.6820 (mtm)
REVERT: A  533 LYS cc_start: 0.7998 (mttm) cc_final: 0.7745 (mttm)
REVERT: A  545 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7865 (mm)
REVERT: A  601 LYS cc_start: 0.7607 (tttp) cc_final: 0.7192 (tttp)
REVERT: A  631 MET cc_start: 0.6809 (tpp) cc_final: 0.6294 (tpp)
REVERT: H  121 TYR cc_start: 0.7158 (m-80) cc_final: 0.6859 (m-80)
REVERT: L    4 GLN cc_start: 0.7492 (mp-120) cc_final: 0.7074 (mp10)
REVERT: L   97 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6409 (mm)
  outliers start: 38
  outliers final: 28
  residues processed: 158
  average time/residue: 0.1528
  time to fit residues: 31.9340
Evaluate side-chains
  163 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  557 MET
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue   99 CYS
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue  103 THR
Chi-restraints excluded: chain L residue  105 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 21 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
A 445 ASN
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.145094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.125899 restraints weight = 9051.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.129598 restraints weight = 4566.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.131959 restraints weight = 2860.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5497  Z= 0.154
  Angle     :  0.612   7.526   7464  Z= 0.309
  Chirality :  0.042   0.165    847
  Planarity :  0.004   0.047    905
  Dihedral  :  6.764  61.678    869
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 20.31 %
    Favored  : 73.32 %
  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: -0.80 (0.32), residues: 669
  helix:  1.30 (0.31), residues: 294
  sheet: -0.73 (0.61), residues: 81
  loop : -2.50 (0.31), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.012   0.001   PHE A  73 
 TYR   0.016   0.001   TYR L  50 
 ARG   0.007   0.000   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04476 (  256)
  hydrogen bonds       : angle       4.30035 (  750)
  SS BOND              : bond        0.00630 (    6)
  SS BOND              : angle       1.34461 (   12)
  covalent geometry    : bond        0.00338 ( 5491)
  covalent geometry    : angle       0.61037 ( 7452)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 131
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6300 (ttp80)
REVERT: A  173 TYR cc_start: 0.7372 (m-80) cc_final: 0.7154 (m-80)
REVERT: A  176 MET cc_start: 0.6697 (mmt) cc_final: 0.6438 (mmt)
REVERT: A  386 PHE cc_start: 0.7993 (t80) cc_final: 0.7260 (t80)
REVERT: A  390 MET cc_start: 0.7125 (mtm) cc_final: 0.6794 (mtm)
REVERT: A  463 CYS cc_start: 0.6473 (t) cc_final: 0.5779 (t)
REVERT: A  533 LYS cc_start: 0.7939 (mttm) cc_final: 0.7708 (mttm)
REVERT: A  545 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7854 (mm)
REVERT: A  601 LYS cc_start: 0.7456 (tttp) cc_final: 0.7092 (tttp)
REVERT: A  631 MET cc_start: 0.6768 (tpp) cc_final: 0.6270 (tpp)
REVERT: H  121 TYR cc_start: 0.7120 (m-80) cc_final: 0.6884 (m-80)
REVERT: L   97 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6253 (mm)
  outliers start: 37
  outliers final: 24
  residues processed: 153
  average time/residue: 0.1381
  time to fit residues: 28.3612
Evaluate side-chains
  157 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue  103 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 25 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0470
   chunk 26 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.145550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.126198 restraints weight = 9038.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.130035 restraints weight = 4483.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.132581 restraints weight = 2762.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5497  Z= 0.135
  Angle     :  0.602   7.868   7464  Z= 0.299
  Chirality :  0.041   0.167    847
  Planarity :  0.004   0.046    905
  Dihedral  :  6.610  62.717    869
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 20.48 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.32), residues: 669
  helix:  1.45 (0.31), residues: 293
  sheet: -0.37 (0.62), residues: 78
  loop : -2.47 (0.31), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 254 
 HIS   0.003   0.001   HIS A 115 
 PHE   0.011   0.001   PHE A  73 
 TYR   0.014   0.001   TYR L  50 
 ARG   0.007   0.000   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04154 (  256)
  hydrogen bonds       : angle       4.17666 (  750)
  SS BOND              : bond        0.00543 (    6)
  SS BOND              : angle       1.19666 (   12)
  covalent geometry    : bond        0.00292 ( 5491)
  covalent geometry    : angle       0.60106 ( 7452)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 132
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6293 (ttp80)
REVERT: A  176 MET cc_start: 0.6680 (mmt) cc_final: 0.6402 (mmt)
REVERT: A  386 PHE cc_start: 0.7940 (t80) cc_final: 0.7243 (t80)
REVERT: A  390 MET cc_start: 0.7071 (mtm) cc_final: 0.6810 (mtm)
REVERT: A  463 CYS cc_start: 0.6323 (t) cc_final: 0.5671 (t)
REVERT: A  533 LYS cc_start: 0.7928 (mttm) cc_final: 0.7608 (mttm)
REVERT: A  545 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7837 (mm)
REVERT: A  601 LYS cc_start: 0.7369 (tttp) cc_final: 0.7036 (tttp)
REVERT: A  631 MET cc_start: 0.6792 (tpp) cc_final: 0.6304 (tpp)
REVERT: H  121 TYR cc_start: 0.7100 (m-80) cc_final: 0.6891 (m-80)
REVERT: L   97 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6228 (mm)
  outliers start: 37
  outliers final: 27
  residues processed: 155
  average time/residue: 0.1511
  time to fit residues: 31.3449
Evaluate side-chains
  162 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  575 HIS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue  103 THR
Chi-restraints excluded: chain L residue  105 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0970
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   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 365 GLN
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.146395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.127310 restraints weight = 8955.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.131033 restraints weight = 4470.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.133526 restraints weight = 2776.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5497  Z= 0.137
  Angle     :  0.619   8.959   7464  Z= 0.305
  Chirality :  0.042   0.168    847
  Planarity :  0.004   0.046    905
  Dihedral  :  6.446  62.962    867
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 20.65 %
    Favored  : 73.32 %
  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: 669
  helix:  1.48 (0.31), residues: 293
  sheet: -0.79 (0.60), residues: 83
  loop : -2.36 (0.31), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.017   0.001   PHE A 276 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.007   0.000   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04147 (  256)
  hydrogen bonds       : angle       4.12894 (  750)
  SS BOND              : bond        0.00557 (    6)
  SS BOND              : angle       1.26453 (   12)
  covalent geometry    : bond        0.00301 ( 5491)
  covalent geometry    : angle       0.61791 ( 7452)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 135
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6226 (ttp80)
REVERT: A  176 MET cc_start: 0.6715 (mmt) cc_final: 0.6426 (mmt)
REVERT: A  386 PHE cc_start: 0.7925 (t80) cc_final: 0.7231 (t80)
REVERT: A  390 MET cc_start: 0.7105 (mtm) cc_final: 0.6823 (mtm)
REVERT: A  463 CYS cc_start: 0.6332 (t) cc_final: 0.5700 (t)
REVERT: A  533 LYS cc_start: 0.8006 (mttm) cc_final: 0.7665 (mttm)
REVERT: A  545 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7822 (mm)
REVERT: A  601 LYS cc_start: 0.7358 (tttp) cc_final: 0.7020 (tttp)
REVERT: A  631 MET cc_start: 0.6786 (tpp) cc_final: 0.6296 (tpp)
REVERT: H  121 TYR cc_start: 0.7116 (m-80) cc_final: 0.6894 (m-80)
REVERT: L   97 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6328 (mm)
  outliers start: 35
  outliers final: 28
  residues processed: 155
  average time/residue: 0.1433
  time to fit residues: 29.6023
Evaluate side-chains
  164 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  575 HIS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue  105 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0030
   chunk 25 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.146317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.127189 restraints weight = 9041.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.130928 restraints weight = 4477.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.133443 restraints weight = 2782.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5497  Z= 0.138
  Angle     :  0.616   7.459   7464  Z= 0.306
  Chirality :  0.041   0.146    847
  Planarity :  0.004   0.045    905
  Dihedral  :  6.432  63.084    867
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 20.48 %
    Favored  : 73.49 %
  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: -0.56 (0.33), residues: 669
  helix:  1.51 (0.31), residues: 293
  sheet: -0.77 (0.61), residues: 83
  loop : -2.33 (0.31), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 254 
 HIS   0.003   0.001   HIS A 115 
 PHE   0.026   0.001   PHE H  32 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.007   0.000   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04055 (  256)
  hydrogen bonds       : angle       4.08969 (  750)
  SS BOND              : bond        0.00543 (    6)
  SS BOND              : angle       1.31330 (   12)
  covalent geometry    : bond        0.00299 ( 5491)
  covalent geometry    : angle       0.61429 ( 7452)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6185 (ttp80)
REVERT: A  169 TYR cc_start: 0.7120 (t80) cc_final: 0.6875 (t80)
REVERT: A  170 MET cc_start: 0.7670 (ttm) cc_final: 0.7445 (ttm)
REVERT: A  176 MET cc_start: 0.6718 (mmt) cc_final: 0.6426 (mmt)
REVERT: A  386 PHE cc_start: 0.7919 (t80) cc_final: 0.7225 (t80)
REVERT: A  390 MET cc_start: 0.7092 (mtm) cc_final: 0.6823 (mtm)
REVERT: A  463 CYS cc_start: 0.6350 (t) cc_final: 0.5741 (t)
REVERT: A  533 LYS cc_start: 0.8025 (mttm) cc_final: 0.7734 (mttm)
REVERT: A  545 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7801 (mm)
REVERT: A  601 LYS cc_start: 0.7330 (tttp) cc_final: 0.6992 (tttp)
REVERT: A  631 MET cc_start: 0.6776 (tpp) cc_final: 0.6276 (tpp)
REVERT: H  121 TYR cc_start: 0.7114 (m-80) cc_final: 0.6894 (m-80)
REVERT: L   97 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6312 (mm)
  outliers start: 35
  outliers final: 30
  residues processed: 154
  average time/residue: 0.1443
  time to fit residues: 29.8943
Evaluate side-chains
  166 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  575 HIS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue  105 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0570
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
** L   4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.145877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.126615 restraints weight = 8950.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.130367 restraints weight = 4469.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.132859 restraints weight = 2776.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5497  Z= 0.161
  Angle     :  0.636   7.406   7464  Z= 0.318
  Chirality :  0.042   0.184    847
  Planarity :  0.004   0.047    905
  Dihedral  :  6.526  62.844    867
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 20.83 %
    Favored  : 73.32 %
  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: -0.62 (0.32), residues: 669
  helix:  1.42 (0.31), residues: 293
  sheet: -0.66 (0.63), residues: 81
  loop : -2.35 (0.31), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.025   0.001   PHE H  32 
 TYR   0.017   0.001   TYR L  50 
 ARG   0.003   0.000   ARG A 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04298 (  256)
  hydrogen bonds       : angle       4.18639 (  750)
  SS BOND              : bond        0.00665 (    6)
  SS BOND              : angle       1.41958 (   12)
  covalent geometry    : bond        0.00353 ( 5491)
  covalent geometry    : angle       0.63431 ( 7452)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.521 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6239 (ttp80)
REVERT: A  118 MET cc_start: 0.8541 (mtm) cc_final: 0.8331 (mtm)
REVERT: A  169 TYR cc_start: 0.7117 (t80) cc_final: 0.6877 (t80)
REVERT: A  170 MET cc_start: 0.7650 (ttm) cc_final: 0.7429 (ttm)
REVERT: A  176 MET cc_start: 0.6740 (mmt) cc_final: 0.6464 (mmt)
REVERT: A  386 PHE cc_start: 0.7932 (t80) cc_final: 0.7240 (t80)
REVERT: A  390 MET cc_start: 0.7087 (mtm) cc_final: 0.6812 (mtm)
REVERT: A  463 CYS cc_start: 0.6434 (t) cc_final: 0.5835 (t)
REVERT: A  533 LYS cc_start: 0.8019 (mttm) cc_final: 0.7725 (mttm)
REVERT: A  545 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7832 (mm)
REVERT: A  601 LYS cc_start: 0.7401 (tttp) cc_final: 0.7048 (tttp)
REVERT: A  631 MET cc_start: 0.6786 (tpp) cc_final: 0.6285 (tpp)
REVERT: H  121 TYR cc_start: 0.7116 (m-80) cc_final: 0.6889 (m-80)
REVERT: L   97 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6339 (mm)
  outliers start: 34
  outliers final: 29
  residues processed: 153
  average time/residue: 0.1435
  time to fit residues: 29.6873
Evaluate side-chains
  164 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 132
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue  105 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0070
   chunk 63 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 28 optimal weight:    0.4980
   chunk 58 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** L   4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.146656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.127471 restraints weight = 8963.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.131241 restraints weight = 4456.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.133748 restraints weight = 2756.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5497  Z= 0.144
  Angle     :  0.625   7.595   7464  Z= 0.313
  Chirality :  0.042   0.172    847
  Planarity :  0.004   0.046    905
  Dihedral  :  6.466  63.238    867
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 20.83 %
    Favored  : 73.49 %
  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: 669
  helix:  1.44 (0.31), residues: 293
  sheet: -0.78 (0.62), residues: 83
  loop : -2.32 (0.31), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.026   0.001   PHE H  32 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.002   0.000   ARG A 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04151 (  256)
  hydrogen bonds       : angle       4.16920 (  750)
  SS BOND              : bond        0.00590 (    6)
  SS BOND              : angle       1.37838 (   12)
  covalent geometry    : bond        0.00316 ( 5491)
  covalent geometry    : angle       0.62313 ( 7452)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6223 (ttp80)
REVERT: A  169 TYR cc_start: 0.7115 (t80) cc_final: 0.6891 (t80)
REVERT: A  176 MET cc_start: 0.6755 (mmt) cc_final: 0.6467 (mmt)
REVERT: A  386 PHE cc_start: 0.7917 (t80) cc_final: 0.7230 (t80)
REVERT: A  390 MET cc_start: 0.7080 (mtm) cc_final: 0.6814 (mtm)
REVERT: A  463 CYS cc_start: 0.6347 (t) cc_final: 0.5758 (t)
REVERT: A  533 LYS cc_start: 0.8023 (mttm) cc_final: 0.7731 (mttm)
REVERT: A  545 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7825 (mm)
REVERT: A  601 LYS cc_start: 0.7342 (tttp) cc_final: 0.7003 (tttp)
REVERT: A  631 MET cc_start: 0.6786 (tpp) cc_final: 0.6287 (tpp)
REVERT: H  121 TYR cc_start: 0.7123 (m-80) cc_final: 0.6902 (m-80)
REVERT: L   97 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6342 (mm)
  outliers start: 33
  outliers final: 29
  residues processed: 149
  average time/residue: 0.1394
  time to fit residues: 27.8108
Evaluate side-chains
  163 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  575 HIS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  629 SER
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain H residue   20 SER
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue  105 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.3980
   chunk 39 optimal weight:    0.0570
   chunk 42 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0050
   chunk 12 optimal weight:    0.0670
   chunk 64 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.2450

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

Flipped N/Q/H residues before XYZ refinement:
H  42 GLN
** L   4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.149131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.129862 restraints weight = 9072.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.133723 restraints weight = 4496.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.136312 restraints weight = 2774.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5497  Z= 0.105
  Angle     :  0.588   7.714   7464  Z= 0.293
  Chirality :  0.040   0.166    847
  Planarity :  0.004   0.045    905
  Dihedral  :  6.207  64.244    867
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 23.41 %
    Favored  : 72.98 %
  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: -0.43 (0.33), residues: 669
  helix:  1.52 (0.32), residues: 291
  sheet: -0.80 (0.61), residues: 83
  loop : -2.09 (0.32), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 470 
 HIS   0.003   0.001   HIS A 115 
 PHE   0.026   0.001   PHE H  32 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.003   0.000   ARG A 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03485 (  256)
  hydrogen bonds       : angle       3.93877 (  750)
  SS BOND              : bond        0.00403 (    6)
  SS BOND              : angle       1.01080 (   12)
  covalent geometry    : bond        0.00221 ( 5491)
  covalent geometry    : angle       0.58756 ( 7452)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2450.30 seconds
wall clock time: 43 minutes 54.42 seconds (2634.42 seconds total)