Starting phenix.real_space_refine
on Thu Mar  6 09:11:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8phw_17677/03_2025/8phw_17677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8phw_17677/03_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_17677/03_2025/8phw_17677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8phw_17677/03_2025/8phw_17677.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8phw_17677/03_2025/8phw_17677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8phw_17677/03_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.06, per 1000 atoms: 1.13
  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: 1.45
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.61
  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: 1.62

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.20 -     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:             14.510
  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:             0.000
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.890
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.240
-------------------------------------------------------------------------------
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   5491  Z= 0.297
  Angle     :  0.722   6.790   7452  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 

*********************** 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  : 0.514 
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: 0.1505
  time to fit residues: 33.2098
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  : 0.561 
-------------------------------------------------------------------------------
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 = 0.124417 restraints weight = 9027.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.128354 restraints weight = 4462.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.130865 restraints weight = 2753.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
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   5491  Z= 0.183
  Angle     :  0.602   7.545   7452  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 

*********************** 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  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 MET cc_start: 0.7666 (ttm) cc_final: 0.7442 (ttm)
REVERT: A  173 TYR cc_start: 0.7487 (m-80) cc_final: 0.7259 (m-80)
REVERT: A  217 MET cc_start: 0.7926 (mmp) cc_final: 0.7563 (mmp)
REVERT: A  253 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6713 (mtm110)
REVERT: A  386 PHE cc_start: 0.8097 (t80) cc_final: 0.7417 (t80)
REVERT: A  390 MET cc_start: 0.7201 (mtm) cc_final: 0.6844 (mtm)
REVERT: A  417 MET cc_start: 0.6692 (mmm) cc_final: 0.6360 (mmm)
REVERT: A  533 LYS cc_start: 0.7966 (mttm) cc_final: 0.7712 (mttm)
REVERT: A  545 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7850 (mm)
REVERT: A  601 LYS cc_start: 0.7571 (tttp) cc_final: 0.7200 (tttp)
REVERT: A  631 MET cc_start: 0.6747 (tpp) cc_final: 0.6238 (tpp)
REVERT: H   32 PHE cc_start: 0.8268 (t80) cc_final: 0.8034 (t80)
REVERT: L   18 ASP cc_start: 0.6001 (m-30) cc_final: 0.5690 (m-30)
REVERT: L   43 LYS cc_start: 0.7712 (mmtm) cc_final: 0.7506 (mmtm)
  outliers start: 35
  outliers final: 18
  residues processed: 153
  average time/residue: 0.1402
  time to fit residues: 28.9933
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  : 0.499 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 19 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0050
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0970
   chunk 2 optimal weight:    0.0770
   overall best weight:    0.1750

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

Flipped N/Q/H residues before XYZ refinement:
A 445 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.148850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.129680 restraints weight = 9090.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.133425 restraints weight = 4495.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.135705 restraints weight = 2787.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5491  Z= 0.139
  Angle     :  0.554   6.925   7452  Z= 0.280
  Chirality :  0.040   0.168    847
  Planarity :  0.004   0.038    905
  Dihedral  :  6.914  58.870    877
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 18.07 %
    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:  1.21 (0.31), residues: 296
  sheet: -0.82 (0.60), residues: 83
  loop : -2.37 (0.32), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   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 

*********************** 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
  163 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.6257 (ttp-170)
REVERT: A   97 ILE cc_start: 0.7988 (tt) cc_final: 0.7786 (tt)
REVERT: A  386 PHE cc_start: 0.7970 (t80) cc_final: 0.7267 (t80)
REVERT: A  390 MET cc_start: 0.7195 (mtm) cc_final: 0.6828 (mtm)
REVERT: A  533 LYS cc_start: 0.7912 (mttm) cc_final: 0.7691 (mttm)
REVERT: A  545 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7801 (mm)
REVERT: A  601 LYS cc_start: 0.7205 (tttp) cc_final: 0.6899 (tttp)
REVERT: A  631 MET cc_start: 0.6732 (tpp) cc_final: 0.6228 (tpp)
  outliers start: 30
  outliers final: 19
  residues processed: 153
  average time/residue: 0.1564
  time to fit residues: 31.5219
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  : 0.519 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 34 optimal weight:    0.2980
   chunk 19 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 56 optimal weight:    0.3980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 544 ASN
** 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 = 0.3897 r_free = 0.3897 target = 0.146004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.126821 restraints weight = 9316.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.130622 restraints weight = 4642.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.133085 restraints weight = 2866.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5491  Z= 0.192
  Angle     :  0.578   7.673   7452  Z= 0.292
  Chirality :  0.041   0.154    847
  Planarity :  0.004   0.040    905
  Dihedral  :  6.522  59.810    870
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 18.42 %
    Favored  : 75.73 %
  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: -0.59 (0.33), residues: 669
  helix:  1.39 (0.31), residues: 296
  sheet: -0.64 (0.60), residues: 83
  loop : -2.31 (0.32), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 254 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.012   0.001   PHE A  73 
 TYR   0.016   0.001   TYR L  50 
 ARG   0.006   0.000   ARG A 614 

*********************** 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
  160 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6274 (ttp80)
REVERT: A  176 MET cc_start: 0.6607 (mmt) cc_final: 0.6387 (mmt)
REVERT: A  386 PHE cc_start: 0.7953 (t80) cc_final: 0.7240 (t80)
REVERT: A  390 MET cc_start: 0.7081 (mtm) cc_final: 0.6801 (mtm)
REVERT: A  533 LYS cc_start: 0.7898 (mttm) cc_final: 0.7674 (mttm)
REVERT: A  545 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7845 (mm)
REVERT: A  601 LYS cc_start: 0.7376 (tttp) cc_final: 0.7043 (tttp)
REVERT: A  631 MET cc_start: 0.6780 (tpp) cc_final: 0.6294 (tpp)
REVERT: L   97 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6194 (mm)
  outliers start: 34
  outliers final: 24
  residues processed: 147
  average time/residue: 0.1565
  time to fit residues: 30.4296
Evaluate side-chains
  151 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  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  279 LEU
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 55 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.145166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.125958 restraints weight = 9085.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.129604 restraints weight = 4572.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.132082 restraints weight = 2869.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5491  Z= 0.190
  Angle     :  0.583   7.946   7452  Z= 0.292
  Chirality :  0.041   0.165    847
  Planarity :  0.004   0.041    905
  Dihedral  :  6.524  61.003    869
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 19.79 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.52 (0.32), residues: 669
  helix:  1.44 (0.31), residues: 296
  sheet: -0.63 (0.60), residues: 83
  loop : -2.26 (0.32), residues: 290

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   0.011   0.001   PHE A  73 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.003   0.000   ARG A 253 

*********************** 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
  164 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6289 (ttp80)
REVERT: A  176 MET cc_start: 0.6662 (mmt) cc_final: 0.6409 (mmt)
REVERT: A  386 PHE cc_start: 0.7932 (t80) cc_final: 0.7244 (t80)
REVERT: A  390 MET cc_start: 0.7091 (mtm) cc_final: 0.6819 (mtm)
REVERT: A  533 LYS cc_start: 0.7926 (mttm) cc_final: 0.7714 (mttm)
REVERT: A  545 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7820 (mm)
REVERT: A  601 LYS cc_start: 0.7350 (tttp) cc_final: 0.7013 (tttp)
REVERT: A  631 MET cc_start: 0.6796 (tpp) cc_final: 0.6303 (tpp)
REVERT: L   97 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6226 (mm)
  outliers start: 33
  outliers final: 21
  residues processed: 154
  average time/residue: 0.1454
  time to fit residues: 29.8984
Evaluate side-chains
  152 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  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  279 LEU
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  482 ILE
Chi-restraints excluded: chain A residue  545 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   94 THR
Chi-restraints excluded: chain H residue  111 TRP
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:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0670
   chunk 25 optimal weight:    0.1980
   chunk 53 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 57 optimal weight:    0.1980
   chunk 26 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.3518

-------------------------------------------------------------------------------
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 = 0.3910 r_free = 0.3910 target = 0.147178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.127669 restraints weight = 9072.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.131507 restraints weight = 4490.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.134093 restraints weight = 2770.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5491  Z= 0.153
  Angle     :  0.567   8.318   7452  Z= 0.280
  Chirality :  0.040   0.160    847
  Planarity :  0.004   0.040    905
  Dihedral  :  6.227  62.246    867
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 19.62 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.33), residues: 669
  helix:  1.58 (0.31), residues: 296
  sheet: -0.27 (0.61), residues: 78
  loop : -2.19 (0.32), residues: 295

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

*********************** 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
  157 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6286 (ttp80)
REVERT: A  176 MET cc_start: 0.6720 (mmt) cc_final: 0.6425 (mmt)
REVERT: A  386 PHE cc_start: 0.7894 (t80) cc_final: 0.7216 (t80)
REVERT: A  390 MET cc_start: 0.7134 (mtm) cc_final: 0.6843 (mtm)
REVERT: A  533 LYS cc_start: 0.7923 (mttm) cc_final: 0.7609 (mttm)
REVERT: A  545 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7739 (mm)
REVERT: A  601 LYS cc_start: 0.7183 (tttp) cc_final: 0.6869 (tttp)
REVERT: A  631 MET cc_start: 0.6820 (tpp) cc_final: 0.6314 (tpp)
REVERT: L   97 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6223 (mm)
  outliers start: 30
  outliers final: 23
  residues processed: 145
  average time/residue: 0.1414
  time to fit residues: 27.7069
Evaluate side-chains
  152 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue   97 ILE
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  279 LEU
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  482 ILE
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  575 HIS
Chi-restraints excluded: chain A residue  604 THR
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   94 THR
Chi-restraints excluded: chain H residue  111 TRP
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 50 optimal weight:    0.0030
   chunk 44 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.146647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.127183 restraints weight = 8933.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.130973 restraints weight = 4424.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.133542 restraints weight = 2742.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5491  Z= 0.184
  Angle     :  0.578   7.617   7452  Z= 0.289
  Chirality :  0.041   0.152    847
  Planarity :  0.004   0.041    905
  Dihedral  :  6.293  62.080    867
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 20.31 %
    Favored  : 74.70 %
  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: -0.32 (0.33), residues: 669
  helix:  1.57 (0.31), residues: 297
  sheet: -0.27 (0.61), residues: 78
  loop : -2.19 (0.32), residues: 294

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   0.024   0.001   PHE H  32 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.008   0.000   ARG A 614 

*********************** 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
  156 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6276 (ttp80)
REVERT: A  176 MET cc_start: 0.6734 (mmt) cc_final: 0.6443 (mmt)
REVERT: A  386 PHE cc_start: 0.7913 (t80) cc_final: 0.7241 (t80)
REVERT: A  390 MET cc_start: 0.7127 (mtm) cc_final: 0.6844 (mtm)
REVERT: A  533 LYS cc_start: 0.8000 (mttm) cc_final: 0.7671 (mttm)
REVERT: A  545 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7770 (mm)
REVERT: A  601 LYS cc_start: 0.7263 (tttp) cc_final: 0.6929 (tttp)
REVERT: A  631 MET cc_start: 0.6810 (tpp) cc_final: 0.6302 (tpp)
REVERT: L   97 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6270 (mm)
  outliers start: 29
  outliers final: 25
  residues processed: 144
  average time/residue: 0.1427
  time to fit residues: 27.7515
Evaluate side-chains
  153 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue   97 ILE
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  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   94 THR
Chi-restraints excluded: chain H residue  111 TRP
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:    0.8980
   chunk 58 optimal weight:    0.0870
   chunk 25 optimal weight:    0.3980
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 32 optimal weight:    0.2980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.146721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.127245 restraints weight = 9054.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.131109 restraints weight = 4473.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.133582 restraints weight = 2750.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5491  Z= 0.179
  Angle     :  0.582   7.530   7452  Z= 0.290
  Chirality :  0.041   0.143    847
  Planarity :  0.003   0.041    905
  Dihedral  :  6.275  62.357    867
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 19.45 %
    Favored  : 74.70 %
  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: -0.33 (0.32), residues: 669
  helix:  1.57 (0.31), residues: 297
  sheet: -0.21 (0.61), residues: 78
  loop : -2.23 (0.31), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.024   0.001   PHE H  32 
 TYR   0.014   0.001   TYR L  50 
 ARG   0.003   0.000   ARG A 253 

*********************** 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
  160 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6274 (ttp80)
REVERT: A  176 MET cc_start: 0.6758 (mmt) cc_final: 0.6463 (mmt)
REVERT: A  386 PHE cc_start: 0.7908 (t80) cc_final: 0.7239 (t80)
REVERT: A  390 MET cc_start: 0.7129 (mtm) cc_final: 0.6842 (mtm)
REVERT: A  533 LYS cc_start: 0.8022 (mttm) cc_final: 0.7711 (mttm)
REVERT: A  545 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7775 (mm)
REVERT: A  601 LYS cc_start: 0.7226 (tttp) cc_final: 0.6937 (tttp)
REVERT: A  631 MET cc_start: 0.6809 (tpp) cc_final: 0.6296 (tpp)
REVERT: L   97 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6303 (mm)
  outliers start: 34
  outliers final: 28
  residues processed: 147
  average time/residue: 0.1419
  time to fit residues: 28.2645
Evaluate side-chains
  155 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 124
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue   97 ILE
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 30 optimal weight:    0.2980
   chunk 62 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0000
   chunk 5 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5584

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.146246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.126892 restraints weight = 8995.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.130717 restraints weight = 4459.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.133254 restraints weight = 2751.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5491  Z= 0.200
  Angle     :  0.617   9.103   7452  Z= 0.306
  Chirality :  0.042   0.178    847
  Planarity :  0.004   0.042    905
  Dihedral  :  6.337  62.495    867
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 20.14 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.32), residues: 669
  helix:  1.57 (0.31), residues: 289
  sheet: -0.18 (0.61), residues: 78
  loop : -2.16 (0.31), residues: 302

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   0.024   0.001   PHE H  32 
 TYR   0.016   0.001   TYR L  50 
 ARG   0.002   0.000   ARG A 253 

*********************** 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
  158 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A   58 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6301 (ttp80)
REVERT: A  176 MET cc_start: 0.6762 (mmt) cc_final: 0.6472 (mmt)
REVERT: A  386 PHE cc_start: 0.7924 (t80) cc_final: 0.7230 (t80)
REVERT: A  390 MET cc_start: 0.7105 (mtm) cc_final: 0.6816 (mtm)
REVERT: A  533 LYS cc_start: 0.8047 (mttm) cc_final: 0.7754 (mttm)
REVERT: A  545 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7794 (mm)
REVERT: A  601 LYS cc_start: 0.7280 (tttp) cc_final: 0.6980 (tttp)
REVERT: A  631 MET cc_start: 0.6827 (tpp) cc_final: 0.6318 (tpp)
REVERT: L   97 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6403 (mm)
  outliers start: 33
  outliers final: 27
  residues processed: 144
  average time/residue: 0.1361
  time to fit residues: 26.3891
Evaluate side-chains
  153 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue   97 ILE
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  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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 8 optimal weight:    0.0970
   chunk 46 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0870
   chunk 63 optimal weight:    0.6980
   chunk 66 optimal weight:    0.2980
   chunk 59 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 65 optimal weight:    0.3980
   chunk 28 optimal weight:    0.4980
   chunk 58 optimal weight:    0.0010
   chunk 41 optimal weight:    0.0770
   overall best weight:    0.1120

-------------------------------------------------------------------------------
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 = 0.3948 r_free = 0.3948 target = 0.150114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.130847 restraints weight = 9018.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.134683 restraints weight = 4447.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.137223 restraints weight = 2735.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5491  Z= 0.136
  Angle     :  0.571   7.892   7452  Z= 0.280
  Chirality :  0.040   0.163    847
  Planarity :  0.003   0.040    905
  Dihedral  :  5.942  63.462    865
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 21.69 %
    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: -0.15 (0.33), residues: 669
  helix:  1.71 (0.31), residues: 292
  sheet: -0.13 (0.61), residues: 78
  loop : -2.03 (0.32), residues: 299

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   0.025   0.001   PHE H  32 
 TYR   0.009   0.001   TYR A 625 
 ARG   0.002   0.000   ARG A 253 

********************** 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
  147 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
REVERT: A  188 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5962 (tt)
REVERT: A  390 MET cc_start: 0.7084 (mtm) cc_final: 0.6810 (mtm)
REVERT: A  533 LYS cc_start: 0.8045 (mttm) cc_final: 0.7763 (mttm)
REVERT: A  545 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7708 (mm)
REVERT: A  601 LYS cc_start: 0.6956 (tttp) cc_final: 0.6716 (tttp)
REVERT: A  625 TYR cc_start: 0.7180 (t80) cc_final: 0.6965 (t80)
REVERT: A  631 MET cc_start: 0.6817 (tpp) cc_final: 0.6310 (tpp)
REVERT: L   97 ILE cc_start: 0.6741 (OUTLIER) cc_final: 0.6294 (mm)
  outliers start: 23
  outliers final: 19
  residues processed: 138
  average time/residue: 0.1397
  time to fit residues: 26.3456
Evaluate side-chains
  144 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ARG
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  189 VAL
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  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   40 VAL
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   97 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 64 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
H  42 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 = 0.3915 r_free = 0.3915 target = 0.147376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.127710 restraints weight = 9102.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.131530 restraints weight = 4503.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.134108 restraints weight = 2792.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5491  Z= 0.202
  Angle     :  0.602   7.686   7452  Z= 0.299
  Chirality :  0.041   0.170    847
  Planarity :  0.004   0.041    905
  Dihedral  :  6.065  62.653    863
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 22.55 %
    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: -0.21 (0.33), residues: 669
  helix:  1.65 (0.31), residues: 289
  sheet: -0.24 (0.60), residues: 83
  loop : -2.02 (0.32), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 122 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.024   0.001   PHE H  32 
 TYR   0.017   0.001   TYR L  50 
 ARG   0.002   0.000   ARG A 253 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2467.49 seconds
wall clock time: 43 minutes 19.51 seconds (2599.51 seconds total)